├── .pre-commit-config.yaml ├── CITATION.cff ├── LICENSE ├── README.md ├── combine_data_NAMD_GOMC.py ├── docs ├── .DS_Store ├── Makefile ├── _images │ ├── .DS_Store │ ├── CatDCD_instructions │ ├── CatDCD_license │ ├── GOMC_fixed_bond_angles.png │ ├── GOMC_subfolders.png │ ├── Hybrid_MC_MD_BPTI.mp4 │ ├── NAMD_GOMC_folders.png │ ├── NAMD_GOMC_license │ ├── NAMD_subfolders_only_box_0.png │ ├── pyMDMC_GITHUB_2021.bib │ ├── pyMDMC_GITHUB_2021.ris │ ├── pyMDMC_PAPER_2022.bib │ ├── pyMDMC_PAPER_2022.ris │ ├── pyMDMC_ZENODO_2021.bib │ └── pyMDMC_ZENODO_2021.ris ├── _static │ ├── .DS_Store │ └── Hybrid_MC_MD_BPTI.mp4 ├── citing_MDMC_PYTHON.rst ├── conf.py ├── docs-env.yml ├── example_simulation.rst ├── generating_systems.rst ├── index.rst ├── installation.rst ├── make.bat ├── requirements.txt ├── running_analysis_code.rst ├── running_the_simulation.rst ├── setup.py ├── simulation_analysis.rst ├── simulation_output.rst └── simulation_parameters_files.rst ├── namd_gomc-env.yml ├── required_data ├── .DS_Store ├── bin │ ├── .DS_Store │ └── catdcd-4.0b │ │ ├── .DS_Store │ │ ├── LINUX │ │ ├── .DS_Store │ │ └── bin │ │ │ ├── .DS_Store │ │ │ └── catdcd4.0 │ │ │ └── catdcd │ │ ├── LINUXAMD64 │ │ ├── .DS_Store │ │ └── bin │ │ │ ├── .DS_Store │ │ │ └── catdcd4.0 │ │ │ └── catdcd │ │ ├── MACOSX │ │ └── bin │ │ │ └── catdcd4.0 │ │ │ └── catdcd │ │ ├── MACOSXX86 │ │ ├── .DS_Store │ │ └── bin │ │ │ ├── .DS_Store │ │ │ └── catdcd4.0 │ │ │ └── catdcd │ │ ├── SOLARIS2_64 │ │ └── bin │ │ │ └── catdcd4.0 │ │ │ └── catdcd │ │ └── SOLARISX86_64 │ │ └── bin │ │ └── catdcd4.0 │ │ └── catdcd ├── config_files │ ├── GOMC_GCMC.conf │ ├── GOMC_GEMC.conf │ ├── GOMC_NPT.conf │ ├── GOMC_NVT.conf │ └── NAMD.conf └── equilb_box_298K │ ├── GOMC_TIPS3P_FF copy.inp │ ├── GOMC_TIPS3P_FF.inp │ ├── NAMD_TIPS3P_FF.inp │ ├── TIPS3P_box_0.pdb │ ├── TIPS3P_box_0.psf │ ├── TIPS3P_reservoir_box_1.pdb │ └── TIPS3P_reservoir_box_1.psf ├── run_NAMD_GOMC.py ├── user_input_NAMD_GOMC.json └── user_input_combine_data_NAMD_GOMC.json /.pre-commit-config.yaml: -------------------------------------------------------------------------------- 1 | ci: 2 | autofix_commit_msg: | 3 | [pre-commit.ci] auto fixes from pre-commit.com hooks 4 | for more information, see https://pre-commit.ci 5 | autofix_prs: true 6 | autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate' 7 | autoupdate_schedule: weekly 8 | skip: [] 9 | submodules: false 10 | repos: 11 | - repo: https://github.com/pre-commit/pre-commit-hooks 12 | rev: v5.0.0 13 | hooks: 14 | - id: check-yaml 15 | - id: end-of-file-fixer 16 | - id: trailing-whitespace 17 | exclude: setup.cfg 18 | - repo: https://github.com/psf/black 19 | rev: 25.1.0 20 | hooks: 21 | - id: black 22 | args: [--line-length=80] 23 | - repo: https://github.com/pycqa/isort 24 | rev: 6.0.1 25 | hooks: 26 | - id: isort 27 | name: isort (python) 28 | args: [--profile=black, --line-length=80] 29 | -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- 1 | cff-version: 1.2.0 2 | message: "If you use this software, please cite it as below." 3 | authors: 4 | - family-names: Crawford 5 | given-names: Brad 6 | orcid: https://orcid.org/0000-0003-0638-7333 7 | - family-names: Potoff 8 | given-names: Jeffrey 9 | orcid: https://orcid.org/0000-0002-4421-8787 10 | title: py-MCMD: A Python Library for Performing Hybrid Monte Carlo - Molecular Dynamics Simulations with GOMC and NAMD 11 | url: https://doi.org/10.5281/zenodo.5142483 12 | doi: 10.5281/zenodo.5142483 13 | version: 0.0.2 14 | date-released: 2021-7-28 15 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Note: There are 2 different licenses, one (1) for NAMD_GOMC and 2 | one (1) the CatDCD - Concatenate DCD files 3 | 4 | NAMD_GOMC LICENSE: 5 | 6 | GNU GENERAL PUBLIC LICENSE 7 | Version 3, 29 June 2007 8 | 9 | Copyright (C) 2007 Free Software Foundation, Inc. 10 | Everyone is permitted to copy and distribute verbatim copies 11 | of this license document, but changing it is not allowed. 12 | 13 | Preamble 14 | 15 | The GNU General Public License is a free, copyleft license for 16 | software and other kinds of works. 17 | 18 | The licenses for most software and other practical works are designed 19 | to take away your freedom to share and change the works. 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No Surrender of Others' Freedom. 546 | 547 | If conditions are imposed on you (whether by court order, agreement or 548 | otherwise) that contradict the conditions of this License, they do not 549 | excuse you from the conditions of this License. If you cannot convey a 550 | covered work so as to satisfy simultaneously your obligations under this 551 | License and any other pertinent obligations, then as a consequence you may 552 | not convey it at all. For example, if you agree to terms that obligate you 553 | to collect a royalty for further conveying from those to whom you convey 554 | the Program, the only way you could satisfy both those terms and this 555 | License would be to refrain entirely from conveying the Program. 556 | 557 | 13. Use with the GNU Affero General Public License. 558 | 559 | Notwithstanding any other provision of this License, you have 560 | permission to link or combine any covered work with a work licensed 561 | under version 3 of the GNU Affero General Public License into a single 562 | combined work, and to convey the resulting work. The terms of this 563 | License will continue to apply to the part which is the covered work, 564 | but the special requirements of the GNU Affero General Public License, 565 | section 13, concerning interaction through a network will apply to the 566 | combination as such. 567 | 568 | 14. Revised Versions of this License. 569 | 570 | The Free Software Foundation may publish revised and/or new versions of 571 | the GNU General Public License from time to time. Such new versions will 572 | be similar in spirit to the present version, but may differ in detail to 573 | address new problems or concerns. 574 | 575 | Each version is given a distinguishing version number. If the 576 | Program specifies that a certain numbered version of the GNU General 577 | Public License "or any later version" applies to it, you have the 578 | option of following the terms and conditions either of that numbered 579 | version or of any later version published by the Free Software 580 | Foundation. If the Program does not specify a version number of the 581 | GNU General Public License, you may choose any version ever published 582 | by the Free Software Foundation. 583 | 584 | If the Program specifies that a proxy can decide which future 585 | versions of the GNU General Public License can be used, that proxy's 586 | public statement of acceptance of a version permanently authorizes you 587 | to choose that version for the Program. 588 | 589 | Later license versions may give you additional or different 590 | permissions. However, no additional obligations are imposed on any 591 | author or copyright holder as a result of your choosing to follow a 592 | later version. 593 | 594 | 15. Disclaimer of Warranty. 595 | 596 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 597 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 598 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 599 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 600 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 601 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 602 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 603 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 604 | 605 | 16. Limitation of Liability. 606 | 607 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 608 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 609 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 610 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 611 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 612 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 613 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 614 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 615 | SUCH DAMAGES. 616 | 617 | 17. Interpretation of Sections 15 and 16. 618 | 619 | If the disclaimer of warranty and limitation of liability provided 620 | above cannot be given local legal effect according to their terms, 621 | reviewing courts shall apply local law that most closely approximates 622 | an absolute waiver of all civil liability in connection with the 623 | Program, unless a warranty or assumption of liability accompanies a 624 | copy of the Program in return for a fee. 625 | 626 | END OF TERMS AND CONDITIONS 627 | 628 | How to Apply These Terms to Your New Programs 629 | 630 | If you develop a new program, and you want it to be of the greatest 631 | possible use to the public, the best way to achieve this is to make it 632 | free software which everyone can redistribute and change under these terms. 633 | 634 | To do so, attach the following notices to the program. It is safest 635 | to attach them to the start of each source file to most effectively 636 | state the exclusion of warranty; and each file should have at least 637 | the "copyright" line and a pointer to where the full notice is found. 638 | 639 | 640 | Copyright (C) 641 | 642 | This program is free software: you can redistribute it and/or modify 643 | it under the terms of the GNU General Public License as published by 644 | the Free Software Foundation, either version 3 of the License, or 645 | (at your option) any later version. 646 | 647 | This program is distributed in the hope that it will be useful, 648 | but WITHOUT ANY WARRANTY; without even the implied warranty of 649 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 650 | GNU General Public License for more details. 651 | 652 | You should have received a copy of the GNU General Public License 653 | along with this program. If not, see . 654 | 655 | Also add information on how to contact you by electronic and paper mail. 656 | 657 | If the program does terminal interaction, make it output a short 658 | notice like this when it starts in an interactive mode: 659 | 660 | Copyright (C) 661 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 662 | This is free software, and you are welcome to redistribute it 663 | under certain conditions; type `show c' for details. 664 | 665 | The hypothetical commands `show w' and `show c' should show the appropriate 666 | parts of the General Public License. Of course, your program's commands 667 | might be different; for a GUI interface, you would use an "about box". 668 | 669 | You should also get your employer (if you work as a programmer) or school, 670 | if any, to sign a "copyright disclaimer" for the program, if necessary. 671 | For more information on this, and how to apply and follow the GNU GPL, see 672 | . 673 | 674 | The GNU General Public License does not permit incorporating your program 675 | into proprietary programs. If your program is a subroutine library, you 676 | may consider it more useful to permit linking proprietary applications with 677 | the library. If this is what you want to do, use the GNU Lesser General 678 | Public License instead of this License. But first, please read 679 | . 680 | 681 | 682 | 683 | 684 | 685 | 686 | 687 | 688 | 689 | 690 | 691 | 692 | CatDCD - Concatenate DCD LICENSE: 693 | 694 | (see https://www.ks.uiuc.edu/Development/MDTools/catdcd/ and 695 | (https://www.ks.uiuc.edu/Development/MDTools/catdcd/license.html): 696 | 697 | University of Illinois Open Source License 698 | Copyright 2003-2007 Theoretical and Computational Biophysics Group, 699 | All rights reserved. 700 | 701 | Developed by: Theoretical and Computational Biophysics Group 702 | University of Illinois at Urbana-Champaign 703 | http://www.ks.uiuc.edu/ 704 | 705 | Permission is hereby granted, free of charge, to any person obtaining a copy of 706 | this software and associated documentation files (the Software), to deal with 707 | the Software without restriction, including without limitation the rights to 708 | use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 709 | of the Software, and to permit persons to whom the Software is furnished to 710 | do so, subject to the following conditions: 711 | 712 | Redistributions of source code must retain the above copyright notice, 713 | this list of conditions and the following disclaimers. 714 | 715 | Redistributions in binary form must reproduce the above copyright notice, 716 | this list of conditions and the following disclaimers in the documentation 717 | and/or other materials provided with the distribution. 718 | 719 | Neither the names of Theoretical and Computational Biophysics Group, 720 | University of Illinois at Urbana-Champaign, nor the names of its contributors 721 | may be used to endorse or promote products derived from this Software without 722 | specific prior written permission. 723 | 724 | THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 725 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 726 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 727 | THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR 728 | OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, 729 | ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 730 | OTHER DEALINGS WITH THE SOFTWARE. 731 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ## py-MCMD: A Python Library for Performing Hybrid Monte Carlo - Molecular Dynamics Simulations with GOMC and NAMD 2 | -------- 3 | 4 | This Python code enables hybrid molecular dynamics/Monte Carlo (MD/MC) simulations using [NAMD](https://www.ks.uiuc.edu/Research/namd/) and the [GPU Optimized Monte Carlo (GOMC)](http://gomc.eng.wayne.edu) software. 5 | The Python code allows users to switch back and forth between the NAMD and GOMC simulation engines, with one (1) iteration of each NAMD and GOMC consisting of a cycle. The user programs the number of cycles and the number of NAMD and GOMC steps per cycle. Combining the MD/MC simulations allows the best of both types of simulations while minimizing the downsides, and in some cases, enabling simulations that were previously not feasible. This code allows the modification of the NAMD and GOMC control files, maximizing user flexibility and functionality. 6 | 7 | Please see the [py-MCMD Read the Docs](https://py-mcmd.readthedocs.io/en/latest/) webpage for more information and instructions. 8 | -------------------------------------------------------------------------------- /docs/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/docs/.DS_Store -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | PAPER = 8 | BUILDDIR = _build 9 | 10 | # User-friendly check for sphinx-build 11 | ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) 12 | $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) 13 | endif 14 | 15 | # Internal variables. 16 | PAPEROPT_a4 = -D latex_paper_size=a4 17 | PAPEROPT_letter = -D latex_paper_size=letter 18 | ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 19 | # the i18n builder cannot share the environment and doctrees with the others 20 | I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 21 | 22 | .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext 23 | 24 | help: 25 | @echo "Please use \`make ' where is one of" 26 | @echo " html to make standalone HTML files" 27 | @echo " dirhtml to make HTML files named index.html in directories" 28 | @echo " singlehtml to make a single large HTML file" 29 | @echo " pickle to make pickle files" 30 | @echo " json to make JSON files" 31 | @echo " htmlhelp to make HTML files and a HTML help project" 32 | @echo " qthelp to make HTML files and a qthelp project" 33 | @echo " devhelp to make HTML files and a Devhelp project" 34 | @echo " epub to make an epub" 35 | @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" 36 | @echo " latexpdf to make LaTeX files and run them through pdflatex" 37 | @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" 38 | @echo " text to make text files" 39 | @echo " man to make manual pages" 40 | @echo " texinfo to make Texinfo files" 41 | @echo " info to make Texinfo files and run them through makeinfo" 42 | @echo " gettext to make PO message catalogs" 43 | @echo " changes to make an overview of all changed/added/deprecated items" 44 | @echo " xml to make Docutils-native XML files" 45 | @echo " pseudoxml to make pseudoxml-XML files for display purposes" 46 | @echo " linkcheck to check all external links for integrity" 47 | @echo " doctest to run all doctests embedded in the documentation (if enabled)" 48 | 49 | clean: 50 | rm -rf $(BUILDDIR)/* 51 | 52 | html: 53 | $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html 54 | @echo 55 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." 56 | 57 | dirhtml: 58 | $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml 59 | @echo 60 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." 61 | 62 | singlehtml: 63 | $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml 64 | @echo 65 | @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." 66 | 67 | pickle: 68 | $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle 69 | @echo 70 | @echo "Build finished; now you can process the pickle files." 71 | 72 | json: 73 | $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json 74 | @echo 75 | @echo "Build finished; now you can process the JSON files." 76 | 77 | htmlhelp: 78 | $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp 79 | @echo 80 | @echo "Build finished; now you can run HTML Help Workshop with the" \ 81 | ".hhp project file in $(BUILDDIR)/htmlhelp." 82 | 83 | qthelp: 84 | $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp 85 | @echo 86 | @echo "Build finished; now you can run "qcollectiongenerator" with the" \ 87 | ".qhcp project file in $(BUILDDIR)/qthelp, like this:" 88 | @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/mbuild.qhcp" 89 | @echo "To view the help file:" 90 | @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/mbuild.qhc" 91 | 92 | devhelp: 93 | $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp 94 | @echo 95 | @echo "Build finished." 96 | @echo "To view the help file:" 97 | @echo "# mkdir -p $$HOME/.local/share/devhelp/mbuild" 98 | @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/mbuild" 99 | @echo "# devhelp" 100 | 101 | epub: 102 | $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub 103 | @echo 104 | @echo "Build finished. The epub file is in $(BUILDDIR)/epub." 105 | 106 | latex: 107 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 108 | @echo 109 | @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." 110 | @echo "Run \`make' in that directory to run these through (pdf)latex" \ 111 | "(use \`make latexpdf' here to do that automatically)." 112 | 113 | latexpdf: 114 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 115 | @echo "Running LaTeX files through pdflatex..." 116 | $(MAKE) -C $(BUILDDIR)/latex all-pdf 117 | @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." 118 | 119 | latexpdfja: 120 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 121 | @echo "Running LaTeX files through platex and dvipdfmx..." 122 | $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja 123 | @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." 124 | 125 | text: 126 | $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text 127 | @echo 128 | @echo "Build finished. The text files are in $(BUILDDIR)/text." 129 | 130 | man: 131 | $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man 132 | @echo 133 | @echo "Build finished. The manual pages are in $(BUILDDIR)/man." 134 | 135 | texinfo: 136 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo 137 | @echo 138 | @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." 139 | @echo "Run \`make' in that directory to run these through makeinfo" \ 140 | "(use \`make info' here to do that automatically)." 141 | 142 | info: 143 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo 144 | @echo "Running Texinfo files through makeinfo..." 145 | make -C $(BUILDDIR)/texinfo info 146 | @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." 147 | 148 | gettext: 149 | $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale 150 | @echo 151 | @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." 152 | 153 | changes: 154 | $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes 155 | @echo 156 | @echo "The overview file is in $(BUILDDIR)/changes." 157 | 158 | linkcheck: 159 | $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck 160 | @echo 161 | @echo "Link check complete; look for any errors in the above output " \ 162 | "or in $(BUILDDIR)/linkcheck/output.txt." 163 | 164 | doctest: 165 | $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest 166 | @echo "Testing of doctests in the sources finished, look at the " \ 167 | "results in $(BUILDDIR)/doctest/output.txt." 168 | 169 | xml: 170 | $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml 171 | @echo 172 | @echo "Build finished. The XML files are in $(BUILDDIR)/xml." 173 | 174 | pseudoxml: 175 | $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml 176 | @echo 177 | @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." 178 | -------------------------------------------------------------------------------- /docs/_images/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/docs/_images/.DS_Store -------------------------------------------------------------------------------- /docs/_images/CatDCD_instructions: -------------------------------------------------------------------------------- 1 | ============ 2 | Instructions 3 | ============ 4 | 5 | CatDCD - Concatenate DCD software 6 | 7 | Introduction 8 | 9 | Catdcd functions much like the Unix "cat" command: it concatenates DCD files into a single DCD file. You can also use catdcd to write only selected atoms to the final DCD file. Starting with version 4.0, CatDCD is now built as part of the VMD Plugin tree, and shares the same reader/writer with VMD. CatDCD 4.0 can read/write any of the structure/trajectory formats that are supported by VMD by virtue of the plugin interface. 10 | Contact 11 | 12 | If you have questions please send email to vmd@ks.uiuc.edu 13 | Download 14 | 15 | CatDCD 4.0 is now part of the VMD plugin distribution 16 | Download catdcd-4.0b.tar.gz (Pre-compiled binaries for all of the target platforms supported by VMD, (10/23/2009)) 17 | License 18 | 19 | UIUC Open Source License 20 | Documentation 21 | 22 | * catdcd * 23 | * Written by Justin Gullingsrud, based on DCD I/O code from VMD 24 | 25 | * FEATURES * 26 | - catdcd functions much like the Unix "cat" command: it concatenates DCD files 27 | into a single DCD file. It also allows the user to specify which atoms and 28 | which frames should be written into the output file; thus DCD's can be split 29 | as well as combined. 30 | 31 | * USAGE * 32 | CatDCD 4.0 33 | catdcd -o outputfile [-otype ] [-i indexfile] 34 | [-stype ] [-s structurefile] 35 | [-first firstframe] [-last lastframe] [-stride stride] 36 | [-] inputfile1 [-] inputfile2 ... 37 | 38 | Allowed input file types: 39 | cpmd pdb dcd Alchemy AMBERPREP BallStick BiosymCAR Boogie 40 | Cacao CADPAC CHARMm Chem3d-1 Chem3d-2 CSSR FDAT GSTAT Feature 41 | Fractional GAMESSoutput Z-matrix Gaussianoutput HIN Isis MacMolecule 42 | Macromodel MicroWorld MM2Input MM2Output MM3 MMADS MDLMOL MOLIN 43 | MopacCartesian MopacInternal MopacOutput PCModel Quanta ShelX 44 | Spartan SpartanSE SpartanMM Sybyl Sybyl2 Conjure Maccs2d Maccs3d 45 | UniChemXYZ XYZ XED gro g96 trr xtc crd crdbox namdbin binpos 46 | webpdb cube rst7 tinker dlpolyhist lammpstrj xyz cor molden 47 | pqr mol2 car gamess xsf 48 | 49 | Allowed output file types: 50 | pdb dcd trr crd crdbox namdbin binpos rst7 xyz pqr 51 | 52 | OR 53 | 54 | catdcd -o [-i ] [-first first] [-last last] 55 | [-stride stride] ... 56 | 57 | OR 58 | 59 | catdcd -num ... 60 | 61 | -o : Specify the output file for CatDCD. Required, unless -num 62 | is present (see below). 63 | 64 | -num: When present, no output file will be written. Instead, CatDCD prints 65 | the number of frames in each file, then exits. 66 | 67 | -i 68 | indexfile should contain the (zero-based) indices of the atoms in the 69 | dcd files whose coordinates are to appear in the output file. The indices 70 | should be ASCII text, separated by whitespace. 71 | 72 | -first first: Specify the first frame to be written to the output file. 73 | Default is 1 (write starting from the first frame read). 74 | 75 | -last last: Specify the last frame to write. Default is the last frame in 76 | the last file. 77 | 78 | -stride stride: Specify how many frames to skip when writing. Default is 1 79 | (don't skip any frames). 80 | 81 | 82 | * CAVEATS * 83 | The input files may be any combination of charmm or xplor format, and big- 84 | or little-endianness. However, they must all have the same number of atoms. 85 | 86 | The code uses only standard C library commands and should thus be portable to 87 | pretty much anywhere, including non-Unix platforms (I haven't tested this ;-) 88 | 89 | * EXAMPLES * 90 | 91 | catdcd -num eq01.dcd eq02.dcd 92 | 93 | Prints the number of frames in the two DCD files, then the total, 94 | then exits. 95 | 96 | catdcd -o eq_all.dcd eq01.dcd eq02.dcd eq03.dcd 97 | 98 | Combines eq01.dcd, eq02.dcd, and eq03.dcd into eq_all.dcd. 99 | 100 | catdcd -o eq_pro.dcd -i protein.ind eq01.dcd 101 | 102 | Takes only the coordinates corresponding to the indices in 103 | 'protein.ind' from eq01.dcd and writes them to eq_pro.dcd 104 | 105 | catdcd -o eq_first.dcd -first 1000 -last 2000 -stride 10 eq01.dcd eq02.dcd 106 | 107 | After skipping 999 frames, writes the 1000 frame and every 10th 108 | subsequent frame to eq_first.dcd, until a total of 2000 frames 109 | have been read. 110 | 111 | * Installation * 112 | Unpack the distribution package. A directory named catdcd will be created. 113 | Enter that directory and type "make". To use a different compiler or compile 114 | flags, edit the first three definitions in the Makefile. 115 | 116 | New in version 4.0: 117 | * CatDCD is now integrated into the VMD plugin tree and is 118 | compiled as part of the standard plugin builds. 119 | 120 | New in version 3.0: 121 | * Now uses the VMD plugins for file reading. This makes it very easy 122 | to adapt the program to handle other file formats. 123 | * Use of VMD file readers means fixed atoms are handled automatically. 124 | 125 | New in version 2.0: 126 | * New command line interface: The -o option is now required for 127 | setting the output file. 128 | * New -num option to print the number of frames in each file, as well 129 | as the total. 130 | * Fixed a bug in the DCD reading code that caused misreading of the 131 | DELTA parameter for byte-swapped Charmm DCD files; caused floating- 132 | point exceptions on Alpha platforms. 133 | 134 | New in Version 1.3: 135 | * Fixed free of uninitialized pointer when no -i option is set. 136 | * Fixed bug in reading of opposite-endian Charmm-format dcd files. 137 | 138 | New in Version 1.2: 139 | * Fixed serious bug that appeared in 1.1; only frames from the first 140 | input file were being written to the output file. 141 | 142 | New in Version 1.1: 143 | * Added -first, -last, and -stride flags. 144 | * Added version number information to the output. 145 | 146 | 147 | 148 | 149 | Note: There are 2 different licenses, one (1) for NAMD_GOMC and 150 | one (1) the CatDCD - Concatenate DCD files 151 | 152 | 153 | CatDCD - Concatenate DCD LICENSE: 154 | 155 | (see https://www.ks.uiuc.edu/Development/MDTools/catdcd/ and 156 | (https://www.ks.uiuc.edu/Development/MDTools/catdcd/license.html): 157 | 158 | University of Illinois Open Source License 159 | Copyright 2003-2007 Theoretical and Computational Biophysics Group, 160 | All rights reserved. 161 | 162 | Developed by: Theoretical and Computational Biophysics Group 163 | University of Illinois at Urbana-Champaign 164 | http://www.ks.uiuc.edu/ 165 | 166 | Permission is hereby granted, free of charge, to any person obtaining a copy of 167 | this software and associated documentation files (the Software), to deal with 168 | the Software without restriction, including without limitation the rights to 169 | use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 170 | of the Software, and to permit persons to whom the Software is furnished to 171 | do so, subject to the following conditions: 172 | 173 | Redistributions of source code must retain the above copyright notice, 174 | this list of conditions and the following disclaimers. 175 | 176 | Redistributions in binary form must reproduce the above copyright notice, 177 | this list of conditions and the following disclaimers in the documentation 178 | and/or other materials provided with the distribution. 179 | 180 | Neither the names of Theoretical and Computational Biophysics Group, 181 | University of Illinois at Urbana-Champaign, nor the names of its contributors 182 | may be used to endorse or promote products derived from this Software without 183 | specific prior written permission. 184 | 185 | THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 186 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 187 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 188 | THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR 189 | OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, 190 | ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 191 | OTHER DEALINGS WITH THE SOFTWARE. 192 | -------------------------------------------------------------------------------- /docs/_images/CatDCD_license: -------------------------------------------------------------------------------- 1 | Note: There are 2 different licenses, one (1) for NAMD_GOMC and 2 | one (1) the CatDCD - Concatenate DCD files 3 | 4 | 5 | CatDCD - Concatenate DCD LICENSE: 6 | 7 | (see https://www.ks.uiuc.edu/Development/MDTools/catdcd/ and 8 | (https://www.ks.uiuc.edu/Development/MDTools/catdcd/license.html): 9 | 10 | University of Illinois Open Source License 11 | Copyright 2003-2007 Theoretical and Computational Biophysics Group, 12 | All rights reserved. 13 | 14 | Developed by: Theoretical and Computational Biophysics Group 15 | University of Illinois at Urbana-Champaign 16 | http://www.ks.uiuc.edu/ 17 | 18 | Permission is hereby granted, free of charge, to any person obtaining a copy of 19 | this software and associated documentation files (the Software), to deal with 20 | the Software without restriction, including without limitation the rights to 21 | use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 22 | of the Software, and to permit persons to whom the Software is furnished to 23 | do so, subject to the following conditions: 24 | 25 | Redistributions of source code must retain the above copyright notice, 26 | this list of conditions and the following disclaimers. 27 | 28 | Redistributions in binary form must reproduce the above copyright notice, 29 | this list of conditions and the following disclaimers in the documentation 30 | and/or other materials provided with the distribution. 31 | 32 | Neither the names of Theoretical and Computational Biophysics Group, 33 | University of Illinois at Urbana-Champaign, nor the names of its contributors 34 | may be used to endorse or promote products derived from this Software without 35 | specific prior written permission. 36 | 37 | THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 38 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 39 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 40 | THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR 41 | OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, 42 | ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 43 | OTHER DEALINGS WITH THE SOFTWARE. 44 | -------------------------------------------------------------------------------- /docs/_images/GOMC_fixed_bond_angles.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/docs/_images/GOMC_fixed_bond_angles.png -------------------------------------------------------------------------------- /docs/_images/GOMC_subfolders.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/docs/_images/GOMC_subfolders.png -------------------------------------------------------------------------------- /docs/_images/Hybrid_MC_MD_BPTI.mp4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/docs/_images/Hybrid_MC_MD_BPTI.mp4 -------------------------------------------------------------------------------- /docs/_images/NAMD_GOMC_folders.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/docs/_images/NAMD_GOMC_folders.png -------------------------------------------------------------------------------- /docs/_images/NAMD_GOMC_license: -------------------------------------------------------------------------------- 1 | Note: There are 2 different licenses, one (1) for NAMD_GOMC and 2 | one (1) the CatDCD - Concatenate DCD files 3 | 4 | NAMD_GOMC LICENSE: 5 | 6 | GNU GENERAL PUBLIC LICENSE 7 | Version 3, 29 June 2007 8 | 9 | Copyright (C) 2007 Free Software Foundation, Inc. 10 | Everyone is permitted to copy and distribute verbatim copies 11 | of this license document, but changing it is not allowed. 12 | 13 | Preamble 14 | 15 | The GNU General Public License is a free, copyleft license for 16 | software and other kinds of works. 17 | 18 | The licenses for most software and other practical works are designed 19 | to take away your freedom to share and change the works. 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It is safest 635 | to attach them to the start of each source file to most effectively 636 | state the exclusion of warranty; and each file should have at least 637 | the "copyright" line and a pointer to where the full notice is found. 638 | 639 | 640 | Copyright (C) 641 | 642 | This program is free software: you can redistribute it and/or modify 643 | it under the terms of the GNU General Public License as published by 644 | the Free Software Foundation, either version 3 of the License, or 645 | (at your option) any later version. 646 | 647 | This program is distributed in the hope that it will be useful, 648 | but WITHOUT ANY WARRANTY; without even the implied warranty of 649 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 650 | GNU General Public License for more details. 651 | 652 | You should have received a copy of the GNU General Public License 653 | along with this program. If not, see . 654 | 655 | Also add information on how to contact you by electronic and paper mail. 656 | 657 | If the program does terminal interaction, make it output a short 658 | notice like this when it starts in an interactive mode: 659 | 660 | Copyright (C) 661 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 662 | This is free software, and you are welcome to redistribute it 663 | under certain conditions; type `show c' for details. 664 | 665 | The hypothetical commands `show w' and `show c' should show the appropriate 666 | parts of the General Public License. Of course, your program's commands 667 | might be different; for a GUI interface, you would use an "about box". 668 | 669 | You should also get your employer (if you work as a programmer) or school, 670 | if any, to sign a "copyright disclaimer" for the program, if necessary. 671 | For more information on this, and how to apply and follow the GNU GPL, see 672 | . 673 | 674 | The GNU General Public License does not permit incorporating your program 675 | into proprietary programs. If your program is a subroutine library, you 676 | may consider it more useful to permit linking proprietary applications with 677 | the library. If this is what you want to do, use the GNU Lesser General 678 | Public License instead of this License. But first, please read 679 | . 680 | -------------------------------------------------------------------------------- /docs/_images/NAMD_subfolders_only_box_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/docs/_images/NAMD_subfolders_only_box_0.png -------------------------------------------------------------------------------- /docs/_images/pyMDMC_GITHUB_2021.bib: -------------------------------------------------------------------------------- 1 | @Inbook{pyMDMC_GITHUB_2021, 2 | author = "Crawford, B. and Potoff J.", 3 | title = "py-MCMD: A Python Library for Performing Hybrid Monte Carlo - Molecular Dynamics Simulations with GOMC and NAMD", 4 | year = "2021", 5 | url = "https://github.com/GOMC-WSU/py-MCMD" 6 | } 7 | -------------------------------------------------------------------------------- /docs/_images/pyMDMC_GITHUB_2021.ris: -------------------------------------------------------------------------------- 1 | TY - 2 | AU - Crawford, B. 3 | AU - Potoff J. 4 | AU - 5 | AU - 6 | AU - 7 | AU - 8 | ED - 9 | ED - 10 | ED - 11 | PY - 2021 12 | DA - 2021 13 | TI - 14 | BT - 15 | SP - 16 | EP - 17 | PB - 18 | CY - 19 | AB - 20 | SN - 21 | UR - https://github.com/GOMC-WSU/py-MCMD 22 | DO - 23 | ID - pyMDMC_GITHUB_2021 24 | ER - 25 | -------------------------------------------------------------------------------- /docs/_images/pyMDMC_PAPER_2022.bib: -------------------------------------------------------------------------------- 1 | @article{pyMDMC_PAPER_2021, 2 | author = "Soroush Barhaghi, M. and Crawford, B. and Schwing, G. and Hardy D.J. and Stone, J.E. and Schwiebert L. and Potoff J. and and Tajkhorshid E.", 3 | title = "py-MCMD: A Python Library for Performing Hybrid Monte Carlo - Molecular Dynamics Simulations with GOMC and NAMD", 4 | year = "2021", 5 | doi = "https://doi.org/10.1021/acs.jctc.1c00911" 6 | url = "https://pubs.acs.org/doi/10.1021/acs.jctc.1c00911" 7 | } 8 | -------------------------------------------------------------------------------- /docs/_images/pyMDMC_PAPER_2022.ris: -------------------------------------------------------------------------------- 1 | TY - 2 | AU - Soroush Barhaghi, M. 3 | AU - Crawford, B. 4 | AU - Schwing, G. 5 | AU - Hardy D.J. 6 | AU - Stone, J.E. 7 | AU - Schwiebert L. 8 | AU - Potoff J. 9 | ED - Tajkhorshid E. 10 | ED - 11 | ED - 12 | PY - 2022 13 | DA - 2022 14 | TI - 15 | BT - 16 | SP - 17 | EP - 18 | PB - 19 | CY - 20 | AB - 21 | SN - 22 | UR - https://pubs.acs.org/doi/10.1021/acs.jctc.1c00911 23 | DO - https://doi.org/10.1021/acs.jctc.1c00911 24 | ID - pyMDMC_PAPER_2021 25 | ER - 26 | -------------------------------------------------------------------------------- /docs/_images/pyMDMC_ZENODO_2021.bib: -------------------------------------------------------------------------------- 1 | @Inbook{pyMDMC_ZENODO_2021, 2 | author = "Crawford, B. and Potoff J.", 3 | title = "py-MCMD: Initial Release", 4 | year = "2021", 5 | url = "https://doi.org/10.5281/zenodo.5142483" 6 | doi = "10.5281/zenodo.5142483" 7 | } 8 | -------------------------------------------------------------------------------- /docs/_images/pyMDMC_ZENODO_2021.ris: -------------------------------------------------------------------------------- 1 | TY - 2 | AU - Crawford, B. 3 | AU - Potoff J. 4 | AU - 5 | AU - 6 | AU - 7 | AU - 8 | ED - 9 | ED - 10 | ED - 11 | PY - 2021 12 | DA - 2021 13 | TI - 14 | BT - 15 | SP - 16 | EP - 17 | PB - 18 | CY - 19 | AB - 20 | SN - 21 | UR - https://doi.org/10.5281/zenodo.5142483 22 | DO - 10.5281/zenodo.5142483 23 | ID - pyMDMC_ZENODO_2021 24 | ER - 25 | -------------------------------------------------------------------------------- /docs/_static/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/docs/_static/.DS_Store -------------------------------------------------------------------------------- /docs/_static/Hybrid_MC_MD_BPTI.mp4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/docs/_static/Hybrid_MC_MD_BPTI.mp4 -------------------------------------------------------------------------------- /docs/citing_MDMC_PYTHON.rst: -------------------------------------------------------------------------------- 1 | Citing the py-MDMC Python code 2 | ============= 3 | 4 | If you use this code for your research, please cite `the GitHub repository `_ and the zenodo DOI (`_): 5 | 6 | **ACS** 7 | 8 | Crawford, B. and Potoff J. py-MCMD: Initial Release, `_, 2021. 9 | 10 | **BibTeX** 11 | 12 | .. code-block:: bibtex 13 | 14 | @Inbook{pyMDMC_ZENODO_2021, 15 | author = "Crawford, B. and Potoff J.", 16 | title = "py-MCMD: Initial Release", 17 | year = "2021", 18 | url = "https://doi.org/10.5281/zenodo.5142483" 19 | doi = "10.5281/zenodo.5142483" 20 | } 21 | 22 | Download as :download:`BibTeX <_images/pyMDMC_ZENODO_2021.bib>` or :download:`RIS <_images/pyMDMC_ZENODO_2021.ris>` 23 | 24 | **ACS** 25 | 26 | Crawford, B. and Potoff J. py-MCMD: A Python Library for Performing Hybrid Monte Carlo - Molecular Dynamics Simulations with GOMC and NAMD, `_, 2021. 27 | 28 | **BibTeX** 29 | 30 | .. code-block:: bibtex 31 | 32 | @Inbook{pyMDMC_GITHUB_2021, 33 | author = "Crawford, B. and Potoff J.", 34 | title = "py-MCMD: A Python Library for Performing Hybrid Monte Carlo - Molecular Dynamics Simulations with GOMC and NAMD", 35 | year = "2021", 36 | url = "https://github.com/GOMC-WSU/py-MCMD" 37 | } 38 | 39 | Download as :download:`BibTeX <_images/pyMDMC_GITHUB_2021.bib>` or :download:`RIS <_images/pyMDMC_GITHUB_2021.ris>` 40 | 41 | **ACS** 42 | 43 | Soroush Barhaghi, M.; Crawford, B.; Schwing, G.; Hardy D.J.; Stone, J.E.; Schwiebert L.; Potoff J.; Tajkhorshid E. py-MCMD: A Python Library for Performing Hybrid Monte Carlo - Molecular Dynamics Simulations with GOMC and NAMD, `_, 2022. 44 | 45 | **BibTeX** 46 | 47 | .. code-block:: bibtex 48 | 49 | @Inbook{pyMDMC_PAPER_2021, 50 | author = " Soroush Barhaghi, M. and Crawford, B. and Schwing, G. and Hardy D.J. and Stone, J.E. and Schwiebert L. and Potoff J. and and Tajkhorshid E.", 51 | title = "py-MCMD: A Python Library for Performing Hybrid Monte Carlo - Molecular Dynamics Simulations with GOMC and NAMD", 52 | year = "2022", 53 | doi = "https://doi.org/10.1021/acs.jctc.1c00911" 54 | url = "https://pubs.acs.org/doi/10.1021/acs.jctc.1c00911" 55 | } 56 | 57 | Download as :download:`BibTeX <_images/pyMDMC_PAPER_2022.bib>` or :download:`RIS <_images/pyMDMC_PAPER_2022.ris>` 58 | 59 | 60 | We also recommend citing the `Concatenate DCD files (CatDCD) `_ from the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign. 61 | 62 | **ACS** 63 | 64 | Gullingsrud J. CatDCD - Concatenate DCD files version 4.0, https://www.ks.uiuc.edu/Development/MDTools/catdcd, 2009. 65 | 66 | **BibTeX** 67 | 68 | .. code-block:: bibtex 69 | 70 | @Inbook{CatDCD_2009, 71 | author = "Gullingsrud, J.", 72 | title = "CatDCD - Concatenate DCD files version 4.0", 73 | year = "2009", 74 | url = "https://www.ks.uiuc.edu/Development/MDTools/catdcd/" 75 | } 76 | -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # 3 | # NDM documentation build configuration file, created by 4 | # sphinx-quickstart on Wed Oct 1 08:59:12 2014. 5 | # 6 | # This file is execfile()d with the current directory set to its 7 | # containing dir. 8 | # 9 | # Note that not all possible configuration values are present in this 10 | # autogenerated file. 11 | # 12 | # All configuration values have a default; values that are commented out 13 | # serve to show the default. 14 | 15 | import os 16 | import pathlib 17 | import sys 18 | 19 | import mock 20 | 21 | # If extensions (or modules to document with autodoc) are in another directory, 22 | # add these directories to sys.path here. If the directory is relative to the 23 | # documentation root, use os.path.abspath to make it absolute, like shown here. 24 | 25 | MOCK_MODULES = [ 26 | "numpy", 27 | "mdtraj", 28 | "mdtraj.core.element", 29 | "nglview", 30 | "oset", 31 | "parmed", 32 | "parmed.parameters", 33 | "parmed.periodic_table", 34 | "scipy", 35 | "scipy.spatial", 36 | "scipy.constants", 37 | "numpy.linalg", 38 | "sphinxcontrib.video", 39 | "ele", 40 | ] 41 | for mod_name in MOCK_MODULES: 42 | sys.modules[mod_name] = mock.Mock() 43 | 44 | 45 | sys.path.insert(0, os.path.abspath("..")) 46 | # sys.path.insert(0, os.path.abspath('sphinxext')) 47 | 48 | base_path = pathlib.Path(__file__).parent 49 | os.system("python {} --name".format((base_path / "../setup.py").resolve())) 50 | 51 | # -- General configuration ------git ------------------------------------------ 52 | 53 | # If your documentation needs a minimal Sphinx version, state it here. 54 | # needs_sphinx = '1.0' 55 | 56 | # Add any Sphinx extension module names here, as strings. They can be 57 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 58 | # ones. 59 | extensions = [ 60 | "nbsphinx", 61 | "sphinx.ext.mathjax", 62 | "sphinx.ext.autodoc", 63 | "sphinxcontrib.inkscapeconverter", 64 | "sphinxcontrib.video", 65 | "sphinx.ext.viewcode", 66 | "sphinx.ext.intersphinx", 67 | "sphinx.ext.autosummary", 68 | "numpydoc", 69 | ] 70 | 71 | # nbsphinx specific configuration 72 | nbsphinx_execute = "never" 73 | nbsphinx_input_prompt = "%s" 74 | nbsphinx_prompt_width = 1.1 75 | html_scaled_image_link = False 76 | nbsphinx_allow_errors = False 77 | 78 | 79 | # Prolog: Displayed on top of the notebook 80 | 81 | nbsphinx_prolog = r""" 82 | {% set docname = 'docs/' + env.doc2path(env.docname, base=None) %} 83 | .. raw:: html 84 | 85 |
86 |

This page was generated from 87 | {{ docname|e }}. 88 |
Interactive online version: 89 | Binder badge. 90 |

91 |
92 | 93 | .. raw:: latex 94 | 95 | \nbsphinxstartnotebook{\scriptsize\noindent\strut 96 | \textcolor{gray}{The following section was generated from 97 | \sphinxcode{\sphinxupquote{\strut {{ docname | escape_latex }}}} \dotfill}} 98 | 99 | """ 100 | 101 | # Displayed on bottom on notebook 102 | nbsphinx_epilog = r""" 103 | {% set docname = 'docs/' + env.doc2path(env.docname, base=None) %} 104 | 105 | .. raw:: latex 106 | 107 | \nbsphinxstopnotebook{\scriptsize\noindent\strut 108 | \textcolor{gray}{\dotfill\ \sphinxcode{\sphinxupquote{\strut 109 | {{ docname | escape_latex }}}} ends here.}} 110 | """ 111 | 112 | autosummary_generate = True 113 | autodoc_default_flags = [ 114 | "members", 115 | ] 116 | numpydoc_class_members_toctree = False 117 | 118 | # stackoverflow.com/questions/12206334 119 | numpydoc_show_class_members = False 120 | numpydoc_show_inherited_class_members = False 121 | 122 | _python_doc_base = "http://docs.python.org/3.9" 123 | 124 | intersphinx_mapping = { 125 | _python_doc_base: None, 126 | "http://docs.scipy.org/doc/numpy": None, 127 | "http://docs.scipy.org/doc/scipy/reference": None, 128 | "http://scikit-learn.org/stable": None, 129 | } 130 | 131 | # Add any paths that contain templates here, relative to this directory. 132 | templates_path = ["_templates"] 133 | 134 | # The suffix of source filenames. 135 | source_suffix = ".rst" 136 | 137 | # The encoding of source files. 138 | # source_encoding = 'utf-8-sig' 139 | 140 | # The master toctree document. 141 | master_doc = "index" 142 | 143 | # General information about the project. 144 | project = "py-MCMD" 145 | author = "Crawford, B. and Potoff J." 146 | copyright = "2021" 147 | 148 | # The version info for the project you're documenting, acts as replacement for 149 | # |version| and |release|, also used in various other places throughout the 150 | # built documents. 151 | # 152 | 153 | version = "0.0.2" 154 | release = "0.0.2" 155 | 156 | 157 | # The language for content autogenerated by Sphinx. Refer to documentation 158 | # for a list of supported languages. 159 | # language = None 160 | 161 | # There are two options for replacing |today|: either, you set today to some 162 | # non-false value, then it is used: 163 | # today = '' 164 | # Else, today_fmt is used as the format for a strftime call. 165 | # today_fmt = '%B %d, %Y' 166 | 167 | # List of patterns, relative to source directory, that match files and 168 | # directories to ignore when looking for source files. 169 | exclude_patterns = ["_build", "**.ipynb_checkpoints"] 170 | 171 | # The reST default role (used for this markup: `text`) to use for all 172 | # documents. 173 | # default_role = None 174 | 175 | # If true, '()' will be appended to :func: etc. cross-reference text. 176 | # add_function_parentheses = True 177 | 178 | # If true, the current module name will be prepended to all description 179 | # unit titles (such as .. function::). 180 | # add_module_names = True 181 | 182 | # If true, sectionauthor and moduleauthor directives will be shown in the 183 | # output. They are ignored by default. 184 | # show_authors = False 185 | 186 | # The name of the Pygments (syntax highlighting) style to use. 187 | pygments_style = "sphinx" 188 | 189 | # A list of ignored prefixes for module index sorting. 190 | # modindex_common_prefix = [] 191 | 192 | # If true, keep warnings as "system message" paragraphs in the built documents. 193 | # keep_warnings = False 194 | 195 | 196 | # -- Options for HTML output ---------------------------------------------- 197 | 198 | # The theme to use for HTML and HTML Help pages. See the documentation for 199 | # a list of builtin themes. 200 | # html_theme = 'default' 201 | import sphinx_rtd_theme 202 | 203 | html_theme = "sphinx_rtd_theme" 204 | hhtml_theme_path = [sphinx_rtd_theme.get_html_theme_path()] 205 | 206 | # Theme options are theme-specific and customize the look and feel of a theme 207 | # further. For a list of options available for each theme, see the 208 | # documentation. 209 | # html_theme_options = {} 210 | 211 | # Add any paths that contain custom themes here, relative to this directory. 212 | # html_theme_path = [] 213 | 214 | # The name for this set of Sphinx documents. If None, it defaults to 215 | # " v documentation". 216 | # html_title = None 217 | 218 | # A shorter title for the navigation bar. Default is the same as html_title. 219 | # html_short_title = None 220 | 221 | # The name of an image file (relative to this directory) to place at the top 222 | # of the sidebar. 223 | # html_logo = None 224 | 225 | # The name of an image file (within the static path) to use as favicon of the 226 | # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 227 | # pixels large. 228 | # html_favicon = None 229 | 230 | # Add any paths that contain custom static files (such as style sheets) here, 231 | # relative to this directory. They are copied after the builtin static files, 232 | # so a file named "default.css" will overwrite the builtin "default.css". 233 | html_static_path = ["_static"] 234 | 235 | # Add any extra paths that contain custom files (such as robots.txt or 236 | # .htaccess) here, relative to this directory. These files are copied 237 | # directly to the root of the documentation. 238 | # html_extra_path = [] 239 | 240 | # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, 241 | # using the given strftime format. 242 | # html_last_updated_fmt = '%b %d, %Y' 243 | 244 | # If true, SmartyPants will be used to convert quotes and dashes to 245 | # typographically correct entities. 246 | # html_use_smartypants = True 247 | 248 | # Custom sidebar templates, maps document names to template names. 249 | html_sidebars = { 250 | "**": [ 251 | "globaltoc.html", 252 | "sourcelink.html", 253 | "searchbox.html", 254 | "relations.html", 255 | "sourcelink.html", 256 | ], 257 | } 258 | 259 | # Additional templates that should be rendered to pages, maps page names to 260 | # template names. 261 | # html_additional_pages = {} 262 | 263 | # If false, no module index is generated. 264 | # html_domain_indices = True 265 | 266 | # If false, no index is generated. 267 | # html_use_index = True 268 | 269 | # If true, the index is split into individual pages for each letter. 270 | html_split_index = False 271 | 272 | # If true, links to the reST sources are added to the pages. 273 | # html_show_sourcelink = True 274 | 275 | # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. 276 | # html_show_sphinx = True 277 | 278 | # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. 279 | # html_show_copyright = True 280 | 281 | # If true, an OpenSearch description file will be output, and all pages will 282 | # contain a tag referring to it. The value of this option must be the 283 | # base URL from which the finished HTML is served. 284 | # html_use_opensearch = '' 285 | 286 | # This is the file name suffix for HTML files (e.g. ".xhtml"). 287 | # html_file_suffix = None 288 | 289 | # Output file base name for HTML help builder. 290 | htmlhelp_basename = "py-MCMD_doc" 291 | -------------------------------------------------------------------------------- /docs/docs-env.yml: -------------------------------------------------------------------------------- 1 | name: py-MDMD-docs 2 | channels: 3 | - conda-forge 4 | dependencies: 5 | - python=3.9 6 | - sphinx 7 | - ele 8 | - nbsphinx 9 | - lark-parser 10 | - requests 11 | - mock 12 | - anaconda 13 | - sphinxcontrib 14 | - pip: 15 | - sphinx_rtd_theme 16 | - sphinxcontrib-svg2pdfconverter 17 | sphinx: 18 | fail_on_warning: true 19 | -------------------------------------------------------------------------------- /docs/example_simulation.rst: -------------------------------------------------------------------------------- 1 | Example Simulation 2 | =============== 3 | 4 | 5 | Video of Hybrid MD/MC: Inserting Water in BPTI's Binding Pocket 6 | --------------- 7 | 8 | Utilizing the hybrid molecular dynamics (MD)/Monte Carlo (MC) or py-MCMD simulation, water is inserted into the buried binding pocket of the bovine pancreatic trypsin inhibitor (BPTI). The hybrid py-MCMD (NAMD/GOMC) simulation produces water in the binding pocket orders of magnitude faster than when using MD alone. The hybrid simulation is capable of producing faster and more accurate results because the MC moves allow waters to be quickly inserted and do not solely rely on diffusion of water into the BPTI binding pocket. 9 | 10 | The **green** protein and waters (spheres) represent the crystallography data. The **purple** protein and **red/white** water are the simulated system. 11 | 12 | .. raw:: html 13 | 14 | 16 | -------------------------------------------------------------------------------- /docs/generating_systems.rst: -------------------------------------------------------------------------------- 1 | 2 | Generating Systems 3 | ======= 4 | 5 | Traditional Chemical Engineering Systems 6 | ------- 7 | 8 | Traditional chemical engineering systems are not proteins or other molecules requiring multiple residue names per molecule. For these systems, the `Molecular Simulation Design Framework (MoSDeF) `_ software is **capable of generating all the PSF, PDB, and force field files required for the GOMC and NAMD simulations**, covering a variety of different systems. The **MoSDeF** software creates all these files using only tens of lines of Python code. 9 | The **MoSDeF** tools permit simulation reproducibility across a variety of simulation engines, 10 | removing the requirement of expert knowledge in all the engines to repeat, continue, or advance the existing research. 11 | Additionally, the **MoSDeF** software permits the auto-generation of numerous and distinct systems, allowing large-scale screening of materials and chemicals via `Signac `_ to manage the simulations and data. 12 | 13 | The `MoSDeF `_ software ecosystem contains the following packages: 14 | * `mBuild `_ -- A hierarchical, component based molecule builder 15 | 16 | * `foyer `_ -- A package for atom-typing as well as applying and disseminating forcefields 17 | 18 | * `GMSO `_ -- Flexible storage of chemical topology for molecular simulation 19 | 20 | 21 | The using MoSDeF software to setup the GOMC and NAMD simulations, is made even easier via the `GOMC-MoSDeF documentation `_, which contains links to the GOMC Manual, and the `GOMC-MoSDeF tutorial files `_ with `GOMC YouTube tutorial videos `_. The GOMC-MoSDeF's PDB, PSF, and force field files are identical to the NAMD files for the traditional chemical engineering simulations, unless there are fixed bonds and angles in the GOMC force field files. Changing the fixed bonds and angles between the GOMC and NAMD force field files is as simple as changing one (1) variable and rerunning that line of code. 22 | 23 | 24 | 25 | Non-Traditional Chemical Engineering Systems 26 | ------- 27 | 28 | Non-Traditional chemical engineering systems are proteins or other molecules requiring multiple residue names per molecule. Currently, the GOMC-MoSDeF software is not compatible with these systems. Therefore, these systems should be constructed using different software, such as `Visual Molecular Dynamics (VMD) `_, or other similar software. 29 | -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- 1 | 2 | py-MCMD: A Python Library for Performing Hybrid Monte Carlo - Molecular Dynamics Simulations with GOMC and NAMD 3 | -------- 4 | 5 | This Python code enables hybrid molecular dynamics/Monte Carlo (MD/MC) simulations using `NAMD `_ and the `GPU Optimized Monte Carlo (GOMC) `_ software. 6 | The Python code allows users to switch back and forth between the NAMD and GOMC simulation engines, with one (1) iteration of each NAMD and GOMC consisting of a cycle. The user programs the number of cycles and the number of NAMD and GOMC steps per cycle. Combining the MD/MC simulations allows the best of both types of simulations while minimizing the downsides, and in some cases, enabling simulations that were previously not feasible. This code allows the modification of the NAMD and GOMC control files, maximizing user flexibility and functionality. 7 | 8 | 9 | This code distribution also contains the `Concatenate DCD (CatDCD) `_ software. 10 | The py-MCMD Python package consists of two (2) different licenses (:download:`Combined_Licenses <../LICENSE>`), or they are available individually: 11 | 12 | * One (1) license is for the NAMD_GOMC hybrid Python code, which initiates and organizes the individual simulations. 13 | 14 | Download as :download:`NAMD_GOMC_license <_images/NAMD_GOMC_license>` 15 | 16 | .. image:: https://img.shields.io/badge/License-GPLv3-blue.svg 17 | :target: www.gnu.org/licenses/gpl-3.0.en.html 18 | 19 | * One (1) license is for the `Concatenate DCD (CatDCD) `_ software which is used to combine the DCD files produced by the py-MCMD Python package. 20 | 21 | Download as :download:`CatDCD_license <_images/CatDCD_license>` 22 | 23 | 24 | .. toctree:: 25 | installation 26 | simulation_parameters_files 27 | running_the_simulation 28 | simulation_output 29 | simulation_analysis 30 | running_analysis_code 31 | example_simulation 32 | CatDCD_instructions_license 33 | generating_systems 34 | citing_MDMC_PYTHON 35 | -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- 1 | Installation and Other Required Files 2 | ============ 3 | 4 | The hybrid py-MCMD Python code can be downloaded or cloned from the `py-MCMD GitHub repository `_. This hybrid NAMD_GOMC Python code does not require any setup, but does require the proper files as input, which are listed below: 5 | 6 | * **PSF** and **PDB** files. *NOTE: One (1) PSF and PDB file are required for the NPT and NVT ensembles, while two (2) PSF and PDB files are required for the GCMC and GEMC ensembles.* 7 | 8 | * **Force field (.inp or .par) files** 9 | 10 | * **NAMD binary files** for the CPU and GPU version, depending on which one you plan on using. *NOTE: NAMD provides two (2) different downloads, one (1) for the CPU version and one (1) for the GPU version.* 11 | 12 | * **GOMC binary files** are automatically built for all the ensembles when compiling GOMC. The CPU version of GOMC is always built, while the GPU version of GOMC is only compiled if the proper CUDA version is installed and accessible during the building process. 13 | 14 | 15 | This Python code is currently compatible only with `NAMD version 2.14 `_ and `GOMC-development branch `_. The NAMD and GOMC software needs to be installed before using this hybrid python code. Please refer to the NAMD and GOMC software instructions for installing them and building the binary files. Please also see the `GOMC Manual `_ and the `NAMD Users Guide `_. These binary files can be moved to a different directory, as this directory is specified in the hybrid simulation input. 16 | 17 | 18 | * In NAMD, the binary file is typically located in the *NAMD_version_OS-CPUorGPU/* directory, named *namd2*. 19 | *NOTE: the user will need to specify the NAMD binary file directory and file name in this python code variables.* 20 | 21 | * For GOMC, the binary files are typically located *GOMC_version_No/bin* directory. The CPU versions of the binary files are named GOMC_CPU_GCMC, GOMC_CPU_GEMC, GOMC_CPU_NPT, and GOMC_CPU_NVT. The GPU versions of the files are named GOMC_GPU_GCMC, GOMC_GPU_GEMC, GOMC_GPU_NPT, and GOMC_GPU_NVT. 22 | *NOTE: the user just needs to specify the GOMC binary directory since this Python code will select the proper binary file.* 23 | 24 | 25 | **NOTE: This code was only tested on Linux operating systems. It was not tested using the Windows, Mac, or other operating systems, so it may not function properly on these operating systems.** 26 | 27 | 28 | **NOTE: A bug exists when running the NAMD simulations in GPU mode with the hybrid GEMC ensemble. It is currently unclear if this is an issue with NAMD, CUDA, or a precision error since the NAMD simulations run perfectly in CPU mode. A temporary workaround when using the hybrid GEMC ensemble is to run GOMC in GPU mode and NAMD in CPU mode.** 29 | 30 | **NOTE: ONLY run NAMD in the NVT ensemble, as running NAMD in the NPT ensemble will cause errors in the box positioning since NAMD and GOMC have different box centering algorithms when centering the box during box size changes.** 31 | 32 | **NOTE:** GOMC does not currently use improper or Urey—Bradley potentials, so if the hybrid simulations contain impropers or Urey—Bradleys, the NAMD simulation energies will be different. In a protein simulation, it should be OK not to use impropers or Urey-Bradleys in GOMC and utilize them in NAMD since the protein will not move in the GOMC simulation due to its size. Each simulation will need to be individually evaluated to determine if not having the impropers or Urey-Bradleys in GOMC is irrelevant or significant to the simulation results.** 33 | -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | REM Command file for Sphinx documentation 4 | 5 | if "%SPHINXBUILD%" == "" ( 6 | set SPHINXBUILD=sphinx-build 7 | ) 8 | set BUILDDIR=_build 9 | set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . 10 | set I18NSPHINXOPTS=%SPHINXOPTS% . 11 | if NOT "%PAPER%" == "" ( 12 | set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% 13 | set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% 14 | ) 15 | 16 | if "%1" == "" goto help 17 | 18 | if "%1" == "help" ( 19 | :help 20 | echo.Please use `make ^` where ^ is one of 21 | echo. html to make standalone HTML files 22 | echo. dirhtml to make HTML files named index.html in directories 23 | echo. singlehtml to make a single large HTML file 24 | echo. pickle to make pickle files 25 | echo. json to make JSON files 26 | echo. htmlhelp to make HTML files and a HTML help project 27 | echo. qthelp to make HTML files and a qthelp project 28 | echo. devhelp to make HTML files and a Devhelp project 29 | echo. epub to make an epub 30 | echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter 31 | echo. text to make text files 32 | echo. man to make manual pages 33 | echo. texinfo to make Texinfo files 34 | echo. gettext to make PO message catalogs 35 | echo. changes to make an overview over all changed/added/deprecated items 36 | echo. xml to make Docutils-native XML files 37 | echo. pseudoxml to make pseudoxml-XML files for display purposes 38 | echo. linkcheck to check all external links for integrity 39 | echo. doctest to run all doctests embedded in the documentation if enabled 40 | goto end 41 | ) 42 | 43 | if "%1" == "clean" ( 44 | for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i 45 | del /q /s %BUILDDIR%\* 46 | goto end 47 | ) 48 | 49 | 50 | %SPHINXBUILD% 2> nul 51 | if errorlevel 9009 ( 52 | echo. 53 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 54 | echo.installed, then set the SPHINXBUILD environment variable to point 55 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 56 | echo.may add the Sphinx directory to PATH. 57 | echo. 58 | echo.If you don't have Sphinx installed, grab it from 59 | echo.http://sphinx-doc.org/ 60 | exit /b 1 61 | ) 62 | 63 | if "%1" == "html" ( 64 | %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html 65 | if errorlevel 1 exit /b 1 66 | echo. 67 | echo.Build finished. The HTML pages are in %BUILDDIR%/html. 68 | goto end 69 | ) 70 | 71 | if "%1" == "dirhtml" ( 72 | %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml 73 | if errorlevel 1 exit /b 1 74 | echo. 75 | echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. 76 | goto end 77 | ) 78 | 79 | if "%1" == "singlehtml" ( 80 | %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml 81 | if errorlevel 1 exit /b 1 82 | echo. 83 | echo.Build finished. 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The XML files are in %BUILDDIR%/xml. 231 | goto end 232 | ) 233 | 234 | if "%1" == "pseudoxml" ( 235 | %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml 236 | if errorlevel 1 exit /b 1 237 | echo. 238 | echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. 239 | goto end 240 | ) 241 | 242 | :end 243 | -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- 1 | numpydoc 2 | sphinx 3 | sphinx_rtd_theme 4 | widgetsnbextension 5 | ipywidgets 6 | sphinxcontrib-svg2pdfconverter 7 | ipykernel 8 | nbsphinx 9 | mock 10 | ele 11 | -------------------------------------------------------------------------------- /docs/running_analysis_code.rst: -------------------------------------------------------------------------------- 1 | Running the Combining Data Code 2 | =============== 3 | 4 | The simulation data combining code is run via Python and combines all the required data into a few files for an easy simulation analysis. The data combining code is located in the main directory (i.e., *"py-MCMD/combine_data_NAMD_GOMC.py"*). Before running the data combining code, the user will need to fill out the proper input variables in the *"user_input_combine_data_NAMD_GOMC.json"* file, located in the same directory since this file determines how the data combining code is processed. The *"user_input_combine_data_NAMD_GOMC.json"* file name can be changed to whatever the user desires. 5 | 6 | 7 | This code is designed to combine the hybrid simulation data into a central location. However, it can also be used to generate the same file types for a traditional NAMD-only or GOMC-only simulation, so the user can easily compare between the simulations. 8 | 9 | 10 | Executing the Combine Data Code 11 | --------------- 12 | 13 | The combine data code is run from its file directory via a terminal window. 14 | 15 | **NOTE:** If the *"user_input_combine_data_NAMD_GOMC.json"* file variables are not set properly for the type of simulation that was conducted, the output will not work, or data will be missing. 16 | 17 | .. code:: ipython3 18 | 19 | cd "directory_containing_run_NAMD_GOMC.py" 20 | 21 | python combine_data_NAMD_GOMC.py -f user_input_combine_data_NAMD_GOMC.json -w combined_data -o False 22 | 23 | 24 | Flags for Combining Data Code 25 | --------------- 26 | 27 | * **-f** *or* **--file** flag : json file 28 | Defines the json file to use for variable inputs to the hybrid NAMD/GOMC, NAMD-only, or GOMC-only combining code. 29 | 30 | * **-w** *or* **--write_folder_name** flag : str 31 | Defines the folder name which is created and contains the all the combined data files. 32 | 33 | * **-o** *or* **--overwrite** flag : (True, true, T, t, False, false, F, or f), default = False 34 | Determines whether to overwrite an exiting combined data folder and data, if they exist. 35 | -------------------------------------------------------------------------------- /docs/running_the_simulation.rst: -------------------------------------------------------------------------------- 1 | Running the Simulation 2 | =============== 3 | 4 | The hybrid py-MCMD simulation can be conducted once the *"user_input_NAMD_GOMC.json"* file is properly filled out to the user's specifications, including generating or obtaining the proper PSF, PDB, and force field (.inp or .par files) and specifying their proper paths. 5 | 6 | **WARNING:** Any hybrid simulation that encounters a NAMD simulation with zero atoms or non-fixed atoms will fail. This failure will likely appear as a seg-fault in GOMC. Currently, these types of simulations are not possible with this software. 7 | 8 | Example # 1: GEMC Ensemble 9 | --------------- 10 | 11 | Use a terminal window and move to the directory which contains the *run_NAMD_GOMC.py* file. Then run hybrid py-MCMD simulations with the NAMD simulations for box 0 and box 1 executed in parallel (assuming both boxes are being simulated in NAMD per the *“user_input_NAMD_GOMC.json”* file). 12 | 13 | .. code:: ipython3 14 | 15 | cd "directory_containing_run_NAMD_GOMC.py" 16 | 17 | python run_NAMD_GOMC.py -f user_input_NAMD_GOMC.json -namd_sims_order parallel 18 | 19 | 20 | 21 | Example # 2: GCMC Ensemble 22 | --------------- 23 | 24 | Use a terminal window and move to the directory which contains the *run_NAMD_GOMC.py* file. Then run hybrid py-MCMD simulations. 25 | 26 | **NOTE:** The NAMD simulations default too in series, but it does not matter since the GCMC simulations box 1 is solely used as a reservoir without the need to evaluate the box's dynamics. 27 | 28 | .. code:: ipython3 29 | 30 | cd "directory_containing_run_NAMD_GOMC.py" 31 | 32 | python run_NAMD_GOMC.py -f user_input_NAMD_GOMC.json 33 | 34 | 35 | Flags for Running the Hybrid Simulation 36 | --------------- 37 | 38 | The flags for running the *run_NAMD_GOMC.py* file user_input_variables_NAMD_GOMC.json file, or whatever the user names it. 39 | 40 | -f *or* --file : json file 41 | Defines the variable inputs file used for the hybrid NAMD/GOMC simulation script. 42 | This file, the *"user_input_variables_NAMD_GOMC.json"* file, is required 43 | to run the hybrid simulation. 44 | 45 | -namd_sims_order *or* --namd_simulation_order : default='series', (options: 'series' or 'parallel') 46 | This sets the NAMD simulation to be run in series or parallel. The data is entered only as series or parallel (default = series). This is only relevant for the GEMC ensemble when utilizing two (2) NAMD simulation boxes (i.e., only_use_box_0_for_namd_for_gemc = False --> both box 0 and box 1). The GCMC, NVT, NPT, or the GEMC ensembles when using only one (1) NAMD simulation box (i.e., only_use_box_0_for_namd_for_gemc = True --> only box 0) are always run in series, since there is nothing to run in parallel. Note: This feature was added so the user can minimize the load on the GPU by running both NAMD simulations in parallel. 47 | -------------------------------------------------------------------------------- /docs/setup.py: -------------------------------------------------------------------------------- 1 | """NAMD_GOMC - A Hybrid MD/MC Simulation Software""" 2 | 3 | import os 4 | import subprocess 5 | from distutils.spawn import find_executable 6 | 7 | from setuptools import find_packages, setup 8 | 9 | ##################################### 10 | NAME = "py-MCMD" 11 | VERSION = "0.0.2" 12 | ISRELEASED = True 13 | if ISRELEASED: 14 | __version__ = VERSION 15 | else: 16 | __version__ = VERSION + ".dev0" 17 | ##################################### 18 | 19 | 20 | def proto_procedure(): 21 | # Find the Protocol Compiler and compile protocol buffers 22 | # Taken from https://github.com/protocolbuffers/protobuf/blob/fcfc47d405113b59bd43c2e54daf5d9fe5c44593/python/setup.py 23 | # Only compile if a protocompiler is found, otherwise don't do anything 24 | if "PROTOC" in os.environ and os.path.exists(os.environ["PROTOC"]): 25 | protoc = os.environ["PROTOC"] 26 | elif os.path.exists("../src/protoc"): 27 | protoc = "../src/protoc" 28 | elif os.path.exists("../src/protoc.exe"): 29 | protoc = "../src/protoc.exe" 30 | elif os.path.exists("../vsprojects/Debug/protoc.exe"): 31 | protoc = "../vsprojects/Debug/protoc.exe" 32 | elif os.path.exists("../vsprojects/Release/protoc.exe"): 33 | protoc = "../vsprojects/Release/protoc.exe" 34 | else: 35 | protoc = find_executable("protoc") 36 | if protoc is None: 37 | protoc = find_executable("protoc.exe") 38 | 39 | if protoc is not None: 40 | compile_proto(protoc) 41 | 42 | 43 | def compile_proto(protoc): 44 | protoc_command = [ 45 | protoc, 46 | "-I=py-MCMD/formats/", 47 | "--python_out=py-MCMD/formats/", 48 | "compound.proto", 49 | ] 50 | subprocess.call(protoc_command) 51 | 52 | 53 | if __name__ == "__main__": 54 | 55 | proto_procedure() 56 | 57 | setup( 58 | name=NAME, 59 | version=__version__, 60 | description=__doc__.split("\n"), 61 | long_description=__doc__, 62 | author="", 63 | author_email="", 64 | url="https://github.com/GOMC-WSU/py-MCMD", 65 | download_url="https://github.com/GOMC-WSU/py-MCMD/tarball/{}".format( 66 | __version__ 67 | ), 68 | packages=find_packages(), 69 | package_data={ 70 | "NAMD_GOMC": [ 71 | "utils/reference/*.{pdb,mol2}", 72 | "lib/*.{pdb,mol2}", 73 | ] 74 | }, 75 | package_dir={"py-MCMD": "py-MCMD"}, 76 | include_package_data=True, 77 | license="GPL-3.0", 78 | zip_safe=False, 79 | keywords="py-MCMD", 80 | classifiers=[ 81 | "Development Status :: 0 - Beta", 82 | "Intended Audience :: Science/Research", 83 | "Intended Audience :: Developers", 84 | "License :: OSI Approved :: GPL-3.0 and a University of Illinois Open Source License", 85 | "Natural Language :: English", 86 | "Programming Language :: Python", 87 | "Programming Language :: Python :: 3", 88 | "Topic :: Scientific/Engineering :: Chemistry", 89 | "Operating System :: Unix", 90 | ], 91 | ) 92 | -------------------------------------------------------------------------------- /docs/simulation_analysis.rst: -------------------------------------------------------------------------------- 1 | Simulation Analysis (post-simulation) 2 | =============== 3 | 4 | The post-simulation analysis is required to combine all the individual simulation files into the combined molecular trajectories or coordinate (DCD file), system Energies and State properties. The systems topology (PSF) file is not combined, but selected and copied to the combined data folder for easy use. 5 | Otherwise, without a data combining code, it would be nearly impossible to sort through all the individual GOMC and NAMD files and combine them all. 6 | The output from the combining file is dependent on the data input file (**user_input_combine_data_NAMD_GOMC.json** file) and the utilized ensemble. The simulation data combining file was designed for these hybrid simulations; however, it also works for the traditional GOMC-only or NAMD-only simulations, so the data is output in the same manner for easy comparison, if needed. The following sections show how the combining data files are output for the hybrid simulations. While the traditional NAMD-only and GOMC-only simulation combined data outputs contain their specific subset of the data. 7 | 8 | 9 | 10 | Hybrid Simulation: NAMD Combined Energy Data 11 | --------------- 12 | 13 | These combined NAMD outputs contain the **Energy and State properties** for the NAMD simulations. Each file also include the header/title, which is only printed once at the top of the files. A few NAMD output files are provided for easy utilization by the user. In these files the energy units are kcal/mol and the density is in g/cm^3. 14 | 15 | * **NAMD_data_box_0.txt** and **NAMD_data_box_1.txt** = The energy rows from each individual NAMD simulation are extracted directly from the NAMD log file and combined into a single file with the corrected time steps. 16 | 17 | * **NAMD_data_density_box_0.txt** and **NAMD_data_density_box_1.txt** = The energy rows from each individual NAMD simulation are extracted directly from the NAMD log file with the **addition of the system density (g/cm^3)** and combined into a single file with the corrected time steps. 18 | 19 | **NOTE:** The box 1 files are only generated for the GEMC ensemble when the user selects NAMD to run both box 0 and box 1. 20 | 21 | 22 | Hybrid Simulation: GOMC Combined Energy Data 23 | --------------- 24 | 25 | The combined GOMC outputs contain the **Energy and State properties** for the GOMC simulations, which are listed in two (2) separate lines (i.e., for example, ENER_0 and STAT_0 for box 0 or ENER_1 and STAT_1 for box 1). 26 | Each file also include the header/title, which is only printed once at the top of the files. 27 | There are several GOMC output files provided so the user has some options. 28 | 29 | **NOTE:** Box 1 is listed as an output in the below examples, is only printed for the GEMC ensemble since box 1 serves no meaning or is not present in the GCMC, NPT, and NVT ensembles. 30 | 31 | 32 | * **GOMC_data_box_0.txt** and **GOMC_data_box_1.txt** = The Energy and Stat data are output for each simulation box as they are extracted exactly as is from the GOMC log file (energy units are in **K** and the density units are in **kg/m^3**). 33 | 34 | 35 | * **GOMC_Energies_Stat_box_0.txt** and **GOMC_Energies_Stat_box_1.txt** = The Energy and Stat data are extracted for each simulation box from the GOMC log file, and they are appended together as a single line with the ENER_X and STAT_X labels removed. The energy units are in **K**, and the density units are in **kg/m^3**. 36 | 37 | 38 | * **GOMC_Energies_Stat_kcal_per_mol_box_0.txt** and **GOMC_Energies_Stat_kcal_per_mol_box_1.txt** = The Energy and Stat data are extracted for each simulation box from the GOMC log file, and they are appended together as a single line with the ENER_X and STAT_X labels removed. The energy units are in **kcal/mol**, and the density units are in **g/cm^3**. 39 | 40 | 41 | Hybrid Simulation: GOMC and NAMD Coordinates/Topology (DCD/PSF) 42 | --------------- 43 | 44 | The GOMC and NAMD coordinate (DCD) and topology (PSF) files can be output using the combining data python code, per the users input. However, for the GCMC and GEMC ensembles, only the PSF and DCD files are output for the GOMC simulation since a NAMD simulation is not currently capable of handling a changing number of atoms. For example, both the combined NAMD and GOMC PSF and DCD files can be output for the NPT and NVT ensembles, but only the GOMC PSF and DCD files can be output for the GCMC and GEMC ensembles. The output will be as follows: 45 | 46 | **NOTE:** The box 1 PSF and DCD files will only be output for the GOMC simulation using the GEMC ensemble. 47 | 48 | * **Output_data_merged.psf** = The topology (PSF) file is used with the combined coordinate (DCD) files to identify the bonds, angles, dihedrals, impropers, and other atoms naming and properties. If this is a GCMC or GEMC ensemble, the topology (PSF) file will contain atoms from both box 0 and box 1. 49 | 50 | 51 | * **combined_box_0_GOMC_dcd_files.dcd** and **combined_box_1_GOMC_dcd_files.dcd** = The combined coordinate (DCD) files from all the individual **GOMC** simulations, or at the selected frequency set by the user input file for combining the data. 52 | 53 | 54 | * **combined_box_0_NAMD_dcd_files.dcd** = The combined coordinate (DCD) files from all the individual **NAMD** simulations, or at the selected frequency set by the user input file for combining the data. This combined NAMD coordinate (DCD) is only output for the NPT and NVT ensembles. 55 | 56 | 57 | 58 | Hybrid GCMC Simulation: GOMC Histogram and Distribution Data 59 | --------------- 60 | 61 | The histogram and distribution data are combined and output only for a GOMC simulation using the GCMC ensemble. Please refer to the `GOMC Manual `_ for more information on the histogram and distribution data. The files are listed as follows. 62 | 63 | * **GOMC_hist_data_box_0.txt** = The combined histogram data for the individual simulations. 64 | 65 | * **GOMC_dist_data_box_0_res_or_mol_no_XXX.txt** = The combined distribution data for each molecule type in the individual simulations. **There will be one (1) combined distribution data file generated for each molecule type in the simulation, and they will replace the no_XXX in the file name with no_1, no_2, etc.** 66 | 67 | 68 | 69 | Hybrid, GOMC-only, or NAMD-only Combining Data Input Variables 70 | --------------- 71 | 72 | These variables are used when running combining the data code for the hybrid MD/MC simulations. However, they can also be used for the traditional GOMC-only or NAMD-only simulations, allowing the user to easily compare between the simulations. The selected variables will determine how the data combining code functions and thus how the data is output. Therefore, the user should ensure that the selected variables are in-line with the simulation which was conducted, or the output data will be lacking or fail to be generated. 73 | 74 | The variables below are contained in the *"user_input_combine_data_NAMD_GOMC.json"* file, which is the in the *"py-MCMD/analysis_combine_data"* directory. When the variables are not used for the particular simulation type ('Hybrid', 'GOMC-only', 'NAMD-only'), the inputs still need to be supplied. However, the only requirement for the unused variables is that a string, boolean, or allowable types and values its requests is provided. The combining file will start and run correctly, provided all the required variables are correct. 75 | 76 | 77 | simulation_type : string (only 'GEMC', 'GCMC', 'NPT', 'NVT') 78 | The simulation type or ensemble to use. 79 | Note: only GEMC-NVT available currently ('GEMC' = GEMC-NVT). 80 | This is required for all combining types ('Hybrid', 'GOMC-only', 'NAMD-only'). 81 | 82 | only_use_box_0_for_namd_for_gemc : bool (true or false) 83 | This chooses if you run both simulation boxes in NAMD 84 | when running the GEMC ensemble, or just box 0. 85 | true = NAMD run only box 0 for GEMC 86 | false = NAMD run box 0 and 1 for GEMC 87 | This input is used when combining the 'Hybrid' data. 88 | This is required when combining the 89 | 'GOMC-only', or 'NAMD-only' data, but is not used. 90 | 91 | simulation_engine_options : string ('Hybrid', 'GOMC-only', 'NAMD-only') 92 | The type of simulation you are combining. 93 | 'Hybrid' is the hybrid NAMD_GOMC simulations. 94 | 'GOMC-only' is stand-alone GOMC simulation. 95 | 'NAMD-only' is stand-alone NAMD simulation. 96 | This is required for all combining types ('Hybrid', 'GOMC-only', 'NAMD-only'). 97 | 98 | gomc_or_namd_only_log_filename : string 99 | The relative path and file name of the log file for the 100 | GOMC-only or NAMD-only simulation, 101 | which is used to create the same file format as the 102 | hybrid simulation combining files. 103 | This input is used when combining the 'GOMC-only', or 'NAMD-only' data. 104 | This is required when combining the 105 | 'Hybrid' data, but is not used. 106 | 107 | combine_namd_dcd_file : bool (true or false) 108 | This chooses if you want combine all the NAMD dcd files into one 109 | file for all the Hybrid NAMD simulations. 110 | This option is only possible for "NVT" and "NPT" ensembles. 111 | true = combine all the NAMD dcd files 112 | false = do not combine all the NAMD dcd files 113 | This input is used when combining the 'Hybrid' data. 114 | This is required when combining the 115 | 'GOMC-only', or 'NAMD-only' data, but is not used. 116 | 117 | combine_gomc_dcd_file : bool (true or false) 118 | This chooses if you want combine all the GOMC dcd files into one 119 | file for all the Hybrid GOMC simulations. 120 | This option available for all the ensembles. 121 | true = combine all the GOMC dcd files 122 | false = do not combine all the GOMC dcd files 123 | This input is used when combining the 'Hybrid' data. 124 | This is required when combining the 125 | 'GOMC-only', or 'NAMD-only' data, but is not used. 126 | 127 | get_initial_gomc_dcd : bool (true or false) 128 | true = This chooses whether to add the initial GOMC dcd trajectory to the combined GOMC dcd files, based on the existing ‘GOMC’ 129 | directory (i.e., the 1st GOMC dcd trajectory in the 1st GOMC individual simulation which are currently in ‘GOMC’ directory). 130 | 131 | false = It will not add the initial dcd file from the first GOMC folder to the combined dcd file. Example: It may be useful to not 132 | include the first folders initial dcd trajectory when users are conducting the piecemeal simulations, deleting the individual simulation 133 | folders as they go. In this example, the user would need to combine the separate dcd files that are created this way outside of this program. 134 | 135 | Note: NAMD does not allow this option; however, when NAMD dcd file are able to be combined (NPT and NVT ensembles). For NAMD, the simulations 136 | starting PDB file can be loaded into the trajectory in VMD or other software, which will allow user to access all the data. 137 | 138 | rel_path_to_combine_binary_catdcd : string 139 | The relative path and file name to the catdcd, which are provided 140 | from the Theoretical and Compuational Biopyysisc group (VMD/NAMD development team) 141 | (https://www.ks.uiuc.edu/Development/MDTools/catdcd/). 142 | This tool is used to combine the dcd files for the hybrid simulations. 143 | *Note: there are various catdcd files for different CPUs and 144 | operating systems, so please select the proper only for your system.* 145 | This input is used when combining the 'Hybrid' data. 146 | This is required when combining the 147 | 'GOMC-only', or 'NAMD-only' data, but is not used. 148 | 149 | rel_path_to_NAMD_and_GOMC_folders : string 150 | The relative path to the main NAMD and GOMC folders which contain 151 | all the individual simulations. This is also where the run_NAMD_GOMC.py 152 | file is located, as it build the NAMD and GOMC folders in the same 153 | directory. 154 | This input is used when combining the 'Hybrid' data. 155 | This is required when combining the 156 | 'GOMC-only', or 'NAMD-only' data, but is not used. 157 | -------------------------------------------------------------------------------- /docs/simulation_output.rst: -------------------------------------------------------------------------------- 1 | Simulation Output 2 | ============ 3 | 4 | The hybrid `py-MCMD `_ Python code generates a few data outputs, which include: 5 | 6 | * A log file for each simulation start/restart. Additionally, one (1) NAMD and one (1) GOMC simulation folder and their output files per cycle, regardless of the number of restarts. Please also see the image below. 7 | 8 | .. image:: _images/NAMD_GOMC_folders.png 9 | :width: 400 10 | 11 | * A *"NAMD"* folder consists of sub-folders containing individual NAMD simulation with it's output files (i.e., 1/2 of a cycle). Each iteration folder is listed in numerical order with the ending of either "_a" or "_b", where "_a" is box 0 and "_b" is box 1 of the previous GOMC simulation (see image below, which shows NAMD simulating only box 0). These individual **NAMD simulation are always even numbered** to keep a trackable order between the simulation engines. Note: box 1 is only applicable to the GEMC ensemble, if the user selects NAMD to run box 1. 12 | 13 | .. image:: _images/NAMD_subfolders_only_box_0.png 14 | :width: 500 15 | 16 | * A *"GOMC"* folder consists of sub-folders containing individual GOMC simulation with it's output files (i.e., 1/2 of a cycle). These individual **GOMC simulation are always odd numbered** to keep a trackable order between the simulation engines (see image below). Note: box 1 is only applicable to the GCMC or GEMC ensembles, in which case, box 0 and box 1 are always contained in the same folder. 17 | 18 | .. image:: _images/GOMC_subfolders.png 19 | :width: 500 20 | 21 | 22 | The hybrid simulation Python code outputs the main NAMD and GOMC folders, each containing 100s to 10,000s of individual simulations and associated files, which are utilized in the *post-simulation analysis* by combining all the files in the individual runs. These individual folders contain **PSF**, **PDB**, **DCD**, **System Energies**, and other **system State properties**, to name a few. 23 | 24 | 25 | **At a minimum, the last completed individual GOMC run is required to restart the simulation; therefore, the user should always keep this file for continuing the simulation from its previous ending point. However, the simulation step numbers are properly calculated/arranged during the post-simulation analysis, and the user may need to correct for this if all the individual simulations are not kept for the final post-simulation analysis.** 26 | 27 | 28 | Retaining all the individual simulation runs can add up to considerable storage requirements. Therefore, we recommended optimizing the number of steps and moves for each simulation engine and calculating the entire run's storage requirements before starting the production runs. *In the future, we plan on programming an auto-cleanup and that will combine all the individual runs on the fly and minimize the storage requirement.* 29 | -------------------------------------------------------------------------------- /docs/simulation_parameters_files.rst: -------------------------------------------------------------------------------- 1 | Simulation Parameters (pre-simulation) 2 | =============== 3 | 4 | 5 | NAMD and GOMC Configuration Files 6 | --------------- 7 | 8 | These are slightly modified versions of the standard configuration files used for the NAMD and GOMC simulation engines. 9 | Some of the variable entries are modified in the configuration files, which allows the python code to search and replace these variables for the next simulation, so the simulation is started correctly from the previous one. 10 | Please refer to the `GOMC Manual `_ and the `NAMD Users Guide `_ for more information on the proper inputs for the simulation engines. 11 | 12 | These files are located in the *"py-MCMD/required_data/config_files"* directory, and **these configurations files are auto-selected based on the user specified ensemble.** 13 | The NAMD configuration file applies to all the possible ensembles. 14 | The provided GOMC configuration files are named and designed for each different ensemble (NPT, NVT, GCMC, or GEMC), which changes the inputs and move frequencies. 15 | An experienced user can modify these configuration files by changing or adding variables, time steps, move types, and move frequencies, as long as the variables work smoothly between NAMD and GOMC. 16 | These changes will **likely** not effect the hybrid python code if the inputs match between NAMD and GOMC and are hardcoded and not dependent on a variable value in the existing configuration files. 17 | **However, the configuration files must maintain their names and locations in the "py-MCMD/required_data/config_files" directory.** 18 | 19 | It is also possible to use various configuration files throughout a longer simulation by simply changing the configuration files and restarting the hybrid simulation with the different files in their proper location. For Example, in the grand canonical Monte Carlo (GCMC) ensemble, suppose the first NAMD simulation requires restraining a protein for the first cycle. In this case, the GCMC simulation can insert molecules into the binding pocket before allowing unrestricted movement of the protein. The simulation would then be restarted on the second cycle to the Nth cycle with a different NAMD configuration file without restraining the protein. 20 | *However, the configuration files must maintain their names and locations.* 21 | 22 | 23 | **NOTE:** A simulation cycle is one (1) NAMD simulation and one (1) GOMC simulation. 24 | 25 | **NOTE:** GOMC and NAMD both support the Shift, Switch, and Buckingham potentials, so they can be implemented in these hybrid simulations without issue. 26 | 27 | **NOTE:** These hybrid simulation are currently only designed for orthogonal boxes. 28 | 29 | **NOTE:** GOMC uses the standard Ewald Summation Method, while NAMD utilized the Particle Mesh Ewald (PME) to calculate long-range electrostatics. 30 | 31 | An Example GCMC configuration file for the GOMC engine is provided below. **The configuration file sections that should not be modified without a good understanding of the overall code are listed at DO NOT MODIFY in each section.** The same DO NOT MODIFY statements are listing in the NAMD control file to alert the user. 32 | 33 | .. literalinclude:: ../required_data/config_files/GOMC_GCMC.conf 34 | 35 | 36 | 37 | Required Files for the Hybrid Simulation 38 | --------------- 39 | 40 | The hybrid simulation requires a **PSF**, **PDB**, and **force field files (i.e., .inp or .par files)** to run the simulation, which are required inputs. Typically, only a single **PDB** and **PSF** file are required per simulation box, unless you need a second **PDB** file to fix or restrain the atoms within NAMD, etc. A single or multiple force field files are required for both the NAMD and GOMC simulation engines, which is dependent on the system, and which force fields are being utilized. 41 | 42 | 43 | **NOTE:** GOMC and NAMD force field files can be slightly different, so please refer to their respective manuals/documentation. However, unlike NAMD, GOMC handles fixed bonds and angles in its force field file by replacing bond and angle K-constants with *"999999999999"*. Please also see the image below for this section of the GOMC water force field with fixed bonds and angles. 44 | 45 | .. image:: _images/GOMC_fixed_bond_angles.png 46 | :width: 350 47 | 48 | **NOTE:** Additionally, the impropers and CMAP parameters need to be removed from the GOMC force field files, or GOMC will fail with an error when reading them. 49 | 50 | MD/MC Hybrid Input 51 | --------------- 52 | 53 | The MD/MC Hybrid input file is in the `json `_ format. An example fo the "user_input_NAMD_GOMC.json" file is provided below, and can be renamed by the user. 54 | 55 | .. literalinclude:: ../user_input_NAMD_GOMC.json 56 | :language: json 57 | 58 | 59 | **NOTE:** The hybrid simulation always starts with NAMD and finishes with GOMC in a cycle. If set by the user, the first NAMD simulation will minimize the structure of the system. 60 | 61 | **NOTE:** We assume that the best number of steps for each simulation engine per cycle is the values that, on average, provides two (2) uncorrelated samples for NAMD and two (2) accepted moves for each of the desired GOMC moves. 62 | 63 | 64 | 65 | **Variable definitions** and usage for the *"user_input_variables_NAMD_GOMC.json"* file, or whatever the user names it are provided below: 66 | 67 | total_cycles_namd_gomc_sims : integer 68 | The total number of simulation cycles, where a cycle is a NAMD and 69 | GOMC simulation. 70 | total_cycles_namd_gomc_sims = (NAMD_simulations + GOMC_simulations)/2 71 | 72 | starting_at_cycle_namd_gomc_sims : integer 73 | The cycle number to start the simulations at. 74 | Enter zero for intial simualtion start, or non-zero for a restart. 75 | A new simulation would be started at zero (0). 76 | To restart a simulation, the last full cycle number of the 77 | simulation would be entered. The user may need to delete 1 or more 78 | of the last simulations if the simulation failed prematurely. 79 | 80 | gomc_use_CPU_or_GPU : string (only 'CPU' or 'GPU') 81 | Run the GOMC simulation using the CPU or GPU. 82 | Note: For the NAMD simulation, the user will have to provide the 83 | path to the GPU or CPU NAMD version (i.e., This function does not 84 | set NAMD's CPU or GPU version). 85 | 86 | simulation_type : string (only 'GEMC', 'GCMC', 'NPT', 'NVT') 87 | The simulation type or ensemble to use 88 | Note: only GEMC-NVT available currently: 'GEMC' = GEMC-NVT 89 | 90 | only_use_box_0_for_namd_for_gemc : bool (true or false) 91 | This chooses if you want to run both simulation boxes in NAMD 92 | when running the GEMC ensemble, or just box 0. 93 | true = NAMD runs only box 0 for GEMC 94 | false = NAMD runs box 0 and 1 for GEMC 95 | 96 | no_core_box_0 : integer (> 0) 97 | Number of CPU cores to use for box 0. This is the ONLY place to enter CPU cores for 98 | 'GCMC', 'NPT', 'NVT', and 'GEMC' and only_use_box_0_for_namd_for_gemc = True 99 | Note: The total simulation core = no_core_box_0 + no_core_box_1, when using the 100 | (GEMC' and only_use_box_0_for_namd_for_gemc = False) values. 101 | Note: If using the 'GCMC', 'NPT', 'NVT', or 102 | (GEMC' and only_use_box_0_for_namd_for_gemc = True) ensembles, 103 | the total simulation cores = no_core_box_0, regardless of the no_core_box_1 value. 104 | 105 | no_core_box_1 : integer (>= 0) 106 | Number or CPU cores to use in box 1. This always ZERO for 'GCMC', 'NPT', 'NVT' (>= 0). 107 | Only use when 'GEMC' and only_use_box_0_for_namd_for_gemc = True (> 0) 108 | Note: The total simulation core = no_core_box_0 + no_core_box_1, when using the 109 | (GEMC' and only_use_box_0_for_namd_for_gemc = False) values. 110 | Note: If using the 'GCMC', 'NPT', 'NVT', or 111 | (GEMC' and only_use_box_0_for_namd_for_gemc = True) ensembles, 112 | the total simulation cores = no_core_box_0, regardless of the no_core_box_1 value. 113 | 114 | simulation_temp_k : float or integer 115 | GOMC and NAMD units of temperature are in Kelvin. 116 | 117 | simulation_pressure_bar : float or integer 118 | GOMC and NAMD units of pressure are in bar (1.01325 bar = 1 atm). 119 | 120 | GCMC_ChemPot_or_Fugacity : None or string (only stings are 'ChemPot' or 'Fugacity') 121 | GCMC ensemble only: The variable used in the to control the GCMC ensemble. 122 | Choose either None, 'ChemPot' or 'Fugacity' 123 | 124 | GCMC_ChemPot_or_Fugacity_dict = {str (residue name up to 4 characters): int or float (see below)} 125 | GCMC ensemble only: The selected residue, which is a molecule, its 126 | chemical potential (ChemPot) or fugacity (Fugacity). 127 | GCMC_ChemPot_or_Fugacity_dict = {str (Residue name): int or float 128 | (ChemPots in unit GOMC K units or Fugacity in unit bar)} 129 | NOTE: For a protein, the general residue name of 'PROTA' should be used, which accounts for the whole protein. 130 | NOTE: For a residue that should not be removed, the residue should have the beta value in the PDB file set to 2, 131 | and have the ChemPot set to be -99999999999999999999999999999999999999. 132 | Example Chempot: GCMC_ChemPot_or_Fugacity_dict = {'TIP3': 1000, 'Cl' : -1000, 'Na' : -900} 133 | Example Fugacity (values >=0): GCMC_ChemPot_or_Fugacity_dict = {'TIP3': 1000, 'Cl' : 10, 'Na' : 0} 134 | Example Chempot with a protein: GCMC_ChemPot_or_Fugacity_dict = 135 | { 136 | "TIP3": -4166, 137 | "PROTA":-99999999999999999999999999999999999999, 138 | "POPC":-99999999999999999999999999999999999999, 139 | "POT":-99999999999999999999999999999999999999, 140 | "CLA":-99999999999999999999999999999999999999 141 | } 142 | 143 | namd_minimize_mult_scalar : int (>=0) 144 | The scalar multiple used to get the number of NAMD minimization steps for this 145 | intitial NAMD simulation. 146 | NAMD_minimize steps = namd_run_steps * namd_minimize_mult_scalar 147 | 148 | namd_run_steps : int (>=10) 149 | The number of steps to run each cycle of the NAMD simulation. 150 | Needs to be 10 minimum for now, NEEDS TO BE THE SAME AS THE PREVIOUS SIMULATION, IF RESTARTED! 151 | 152 | gomc_run_steps : int (>=10) 153 | The number of steps to run each cycle of the GOMC simulation. 154 | Needs to be 10 minimum for now, NEEDS TO BE THE SAME AS THE PREVIOUS SIMULATION, IF RESTARTED! 155 | 156 | set_dims_box_0_list : list or null, [null or float or int (>0), null or float or int (>0), null or float or int (>0)] 157 | The x, y, and z-dimensions of length for box 0 in Angstrom units. 158 | This is a list of 3, which can contain a null, float or int (>0). 159 | The length is auto read from the PDB files CRYST1 line, if it is containted there. 160 | This command overrides the PDB value(s), and is needed for the simulation if 161 | the data is not in the pdb file. 162 | Note: if null is used instead of a list the PDB values will be used. 163 | Note: if null is used instead of the x, y, or z-dimension, the 164 | PDB file will be used for the null dimensions. Example: [10, null, null], 165 | the x dimension would use 10 and the y and z dimensions would be the PDB 166 | file values. 167 | 168 | set_dims_box_1_list : list or null, [null or float or int (>0), null or float or int (>0), null or float or int (>0)] 169 | The x, y, and z-dimensions of length for box 1 in Angstrom units. 170 | This is a list of 3, which can contain a null, float or int (>0). 171 | The length is auto read from the PDB files CRYST1 line, if it is containted there. 172 | This command overrides the PDB value(s), and is needed for the simulation if 173 | the data is not in the pdb file. 174 | Note: if null is used instead of a list the PDB values will be used. 175 | Note: if null is used instead of the x, y, or z-dimension, the 176 | PDB file will be used for the null dimensions. Example: [10, null, null], 177 | the x dimension would use 10 and the y and z dimensions would be the PDB 178 | file values. 179 | 180 | set_angle_box_0_list : list or null, [null or float or int, null or float or int, null or float or int] 181 | The alpha, beta, and gamma angles for box 0 in degrees. 182 | This is a list of 3, which can contain a null, float or int. 183 | The angles are auto read from the PDB files CRYST1 line, if it is containted there. 184 | This command overrides the PDB value(s), and is needed for the simulation if 185 | the data is not in the pdb file. 186 | Note: if null is used instead of a list the PDB values will be used. 187 | Note: if null is used instead of the alpha, beta, and gamma angles, the 188 | PDB file will be used for the null dimensions. Example: [10, null, null], 189 | the alpha angle would use 10 and the beta and gamma angles would be the PDB 190 | file values. 191 | NOTE: CURRENTLY ONLY ORTHOGONAL BOXES ARE AVAILABLE, SO ONLY NULL OR 90 192 | WILL BE ACCEPTED. NULL WILL AUTO DEFAUT TO 90. 193 | 194 | set_angle_box_1_list : list or null, [null or float or int, null or float or int, null or float or int] 195 | The alpha, beta, and gamma angles for box 1 in degrees. 196 | This is a list of 3, which can contain a null, float or int. 197 | The angles are auto read from the PDB files CRYST1 line, if it is containted there. 198 | This command overrides the PDB value(s), and is needed for the simulation if 199 | the data is not in the pdb file. 200 | Note: if null is used instead of a list the PDB values will be used. 201 | Note: if null is used instead of the alpha, beta, and gamma angles, the 202 | PDB file will be used for the null dimensions. Example: [10, null, null], 203 | the alpha angle would use 10 and the beta and gamma angles would be the PDB 204 | file values. 205 | NOTE: CURRENTLY ONLY ORTHOGONAL BOXES ARE AVAILABLE, SO ONLY NULL OR 90 206 | WILL BE ACCEPTED. NULL WILL AUTO DEFAUT TO 90. 207 | 208 | starting_ff_file_list_gomc : list of strings 209 | All the force fields for the GOMC simulation. 210 | The strings in the list must be the relative path and file name to the force field(s) 211 | Example : ["required_data/equilb_box_298K/GOMC_TIPS3P_FF.inp", "required_data/equilb_box_298K/GOMC_NaCl_FF.inp"] 212 | 213 | starting_ff_file_list_namd : list of strings 214 | All the force fields for the NAMD simulation. 215 | The strings in the list must be the relative path and file name to the force field(s) 216 | Example : ["required_data/equilb_box_298K/NAMD_TIPS3P_FF.inp", "required_data/equilb_box_298K/NAMD_NaCl_FF.inp"] 217 | 218 | starting_pdb_box_0_file : string 219 | The relative path and filename to the starting PDB file for box 0, 220 | which is initally fed to the NAMD simulation since it starts first. 221 | The string in the list must be the relative path to the force fields and the file name 222 | Example : "required_data/equilb_box_298K/TIPS3P_box_0.pdb" 223 | 224 | starting_psf_box_0_file : string 225 | The relative path and filename to the starting PSF file box 0, 226 | which is initally fed to the NAMD simulation since it starts first. 227 | The string in the list must be the relative path to the force fields and the file name 228 | Example : "required_data/equilb_box_298K/TIPS3P_box_0.psf 229 | 230 | starting_pdb_box_1_file : string 231 | The relative path and filename to the starting PDB file for box 1, 232 | which is initally fed to the NAMD simulation since it starts first. 233 | The string in the list must be the relative path to the force fields and the file name 234 | Note: this is only needed for the "GCMC" and "GEMC" ensembles/simulation types 235 | Example : "required_data/equilb_box_298K/TIPS3P_box_1.pdb" 236 | 237 | starting_psf_box_1_file : string 238 | The relative path and filename to the starting PSF file box 1, 239 | which is initally fed to the NAMD simulation since it starts first. 240 | The string in the list must be the relative path to the force fields and the file name 241 | Note: this is only needed for the "GCMC" and "GEMC" ensembles/simulation types 242 | Example : "required_data/equilb_box_298K/TIPS3P_box_1.psf 243 | 244 | namd_bin_file : string 245 | The relative path to the directory where the namd2 file binary is located. 246 | This should be in the required_data/bin/NAMD212, or required_data/bin/NAMD212 247 | or required_data/bin directory. 248 | IMPORTANT MANUAL MODIFICATION: To use the GPU and CPU or either version of namd, 249 | the copied files in this directory must be renamed namd2_CPU and namd2_GPU. 250 | NOTE: THIS WAS ONLY TESTED ON NAMD VERSION 2.14, SO IT MAY NOT WORK ON OTHER 251 | NAMD VERSIONS WITHOUT SOME CODE MODIFICATION. 252 | Alternatively, a sybolic link to namd2 file binary could be there. 253 | Example: "required_data/bin/NAMD212" 254 | 255 | gomc_bin_file : string 256 | The relative path to the directory where the GOMC file binaries are located. 257 | This should be in the required_data/bin directory. 258 | Alternatively, a sybolic link to GOMC file binaries file binary could be there. 259 | NOTE: THIS WAS ONLY TESTED ON THE GOMC DEVELOPMENT AFTER VERSION 2.70, 260 | SO IT MAY NOT WORK ON OTHER GOMC VERSIONS WITHOUT SOME CODE MODIFICATION, 261 | AND SOME ADDITIONAL FUNCTIONALLITY IS NOT IN PREVIOUS GOMC VERSIONS. 262 | Example: "required_data/bin" 263 | -------------------------------------------------------------------------------- /namd_gomc-env.yml: -------------------------------------------------------------------------------- 1 | name: NAMD_GOMC-code 2 | channels: 3 | - conda-forge 4 | dependencies: 5 | - python=3.9 6 | - sphinx 7 | - ele 8 | - nbsphinx 9 | - lark-parser 10 | - requests 11 | - mock 12 | - argparse 13 | - pandas 14 | - scipy 15 | - bumpy 16 | - subprocess32 17 | - json-c 18 | - glob2 19 | - pip: 20 | - sphinx_rtd_theme 21 | - sphinxcontrib-svg2pdfconverter 22 | sphinx: 23 | fail_on_warning: true 24 | -------------------------------------------------------------------------------- /required_data/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/required_data/.DS_Store -------------------------------------------------------------------------------- /required_data/bin/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/required_data/bin/.DS_Store -------------------------------------------------------------------------------- /required_data/bin/catdcd-4.0b/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/required_data/bin/catdcd-4.0b/.DS_Store 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/required_data/bin/catdcd-4.0b/SOLARIS2_64/bin/catdcd4.0/catdcd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/required_data/bin/catdcd-4.0b/SOLARIS2_64/bin/catdcd4.0/catdcd -------------------------------------------------------------------------------- /required_data/bin/catdcd-4.0b/SOLARISX86_64/bin/catdcd4.0/catdcd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/py-MCMD/d2f2dae61ee76b4d51d12394b0ba56db1aa2db92/required_data/bin/catdcd-4.0b/SOLARISX86_64/bin/catdcd4.0/catdcd -------------------------------------------------------------------------------- /required_data/config_files/GOMC_GCMC.conf: -------------------------------------------------------------------------------- 1 | ######################## 2 | #Control file for GOMC_GCMC 3 | ######################## 4 | 5 | ############################################################################ 6 | # ========-------------------- INPUT --------------------------=========== 7 | ############################################################################ 8 | 9 | ######################### 10 | # enable, step (DO NOT MODIFY or the hybrid simulation and combine files may not work) 11 | ######################### 12 | Restart restart_true_or_false 13 | 14 | Checkpoint Restart_Checkpoint_file 15 | #################################### 16 | # kind {RESTART, RANDOM, INTSEED} (DO NOT MODIFY or the hybrid simulation and combine files may not work) 17 | #################################### 18 | PRNG RANDOM 19 | 20 | #################################### 21 | # FORCE FIELD (DO NOT MODIFY or the hybrid simulation and combine files may not work) 22 | #################################### 23 | ParaTypeCHARMM true 24 | 25 | all_parameter_files 26 | #################################### 27 | # INPUT PDB FILES (DO NOT MODIFY or the hybrid simulation and combine files may not work) 28 | #################################### 29 | Coordinates 0 pdb_file_box_0_file 30 | Coordinates 1 pdb_file_box_1_file 31 | 32 | #################################### 33 | # INPUT PSF FILES (DO NOT MODIFY or the hybrid simulation and combine files may not work) 34 | #################################### 35 | Structure 0 psf_file_box_0_file 36 | Structure 1 psf_file_box_1_file 37 | 38 | #################################### 39 | # INPUT BINARY coodinatd, XSC, velocity files (DO NOT MODIFY or the hybrid simulation and combine files may not work) 40 | #################################### 41 | 42 | binCoordinates 0 coor_box_0_file 43 | extendedSystem 0 xsc_box_0_file 44 | binVelocities 0 vel_box_0_file 45 | 46 | binCoordinates 1 coor_box_1_file 47 | extendedSystem 1 xsc_box_1_file 48 | binVelocities 1 vel_box_1_file 49 | 50 | 51 | ############################################################################ 52 | # =======--------------------- SYSTEM --------------------------=========== 53 | ############################################################################ 54 | ################################## 55 | # Temp, and ChemPots or Fugacities (DO NOT MODIFY or the hybrid simulation and combine files may not work) 56 | ################################## 57 | mu_ChemPot_K_or_P_Fugacitiy_bar_all 58 | Temperature System_temp_set 59 | 60 | ############################# 61 | # SIMULATION CONDITION 62 | ############################# 63 | Potential SWITCH 64 | Rswitch 10.0 65 | LRC false 66 | Rcut 12 67 | RcutLow 1.0 68 | Exclude 1-3 69 | 1-4scaling 1.0 70 | 71 | 72 | ############################# 73 | # ELECTROSTATIC 74 | ############################# 75 | Ewald true 76 | ElectroStatic true 77 | CachedFourier false 78 | Tolerance 0.00001 79 | 80 | 81 | ############################### 82 | # PRESSURE CALCULATION (DO NOT MODIFY or the hybrid simulation and combine files may not work) 83 | ################################ 84 | PressureCalc true GOMC_console_BLKavg_Hist_Steps 85 | 86 | ################################ 87 | # STEPS (DO NOT MODIFY or the hybrid simulation and combine files may not work) 88 | ################################ 89 | InitStep 0 90 | RunSteps GOMC_Run_Steps 91 | EqSteps GOMC_Equilb_Steps 92 | AdjSteps GOMC_Adj_Steps 93 | 94 | 95 | 96 | ################################ 97 | # MOVE FREQUENCY 98 | ################################ 99 | 100 | SwapFreq 1.000 101 | DisFreq 0.000 102 | RotFreq 0.000 103 | RegrowthFreq 0.000 104 | IntraSwapFreq 0.000 105 | 106 | 107 | ################################ 108 | # BOX DIMENSION #, X, Y, Z (DO NOT MODIFY or the hybrid simulation and combine files may not work) 109 | ################################ 110 | CellBasisVector1 0 x_dim_box_0 0.00 0.00 111 | CellBasisVector2 0 0.00 y_dim_box_0 0.00 112 | CellBasisVector3 0 0.00 0.00 z_dim_box_0 113 | 114 | CellBasisVector1 1 x_dim_box_1 0.00 0.00 115 | CellBasisVector2 1 0.00 y_dim_box_1 0.00 116 | CellBasisVector3 1 0.00 0.00 z_dim_box_1 117 | 118 | 119 | 120 | ############################## 121 | # CBMC TRIALS 122 | ############################## 123 | CBMC_First 16 124 | CBMC_Nth 8 125 | CBMC_Ang 50 126 | CBMC_Dih 50 127 | 128 | 129 | ############################################################################ 130 | # =======-------------------- OUTPUT (DO NOT MODIFY or the hybrid simulation and combine files may not work) --------------------------=========== 131 | ############################################################################ 132 | 133 | 134 | ########################## 135 | # statistics filename add (DO NOT MODIFY or the hybrid simulation and combine files may not work) 136 | ########################## 137 | OutputName Output_data 138 | 139 | ##################################### 140 | # enable, frequency (DO NOT MODIFY or the hybrid simulation and combine files may not work) 141 | ##################################### 142 | RestartFreq true GOMC_RST_Coor_CKpoint_Steps 143 | CheckpointFreq true GOMC_RST_Coor_CKpoint_Steps 144 | CoordinatesFreq false GOMC_RST_Coor_CKpoint_Steps 145 | ConsoleFreq true GOMC_console_BLKavg_Hist_Steps 146 | BlockAverageFreq true GOMC_console_BLKavg_Hist_Steps 147 | HistogramFreq true GOMC_console_BLKavg_Hist_Steps 148 | DCDFreq true GOMC_RST_Coor_CKpoint_Steps 149 | 150 | ################################ 151 | # OutHistSettings (DO NOT MODIFY or the hybrid simulation and combine files may not work) 152 | ################################ 153 | DistName dis 154 | HistName his 155 | RunNumber 1 156 | RunLetter a 157 | SampleFreq GOMC_Hist_sample_Steps 158 | 159 | ################################## 160 | # enable: blk avg., fluct. (DO NOT MODIFY or the hybrid simulation and combine files may not work) 161 | ################################## 162 | OutEnergy true true 163 | OutPressure true true 164 | OutMolNum true true 165 | OutDensity true true 166 | OutVolume true true 167 | OutSurfaceTension false false 168 | -------------------------------------------------------------------------------- /required_data/config_files/GOMC_GEMC.conf: -------------------------------------------------------------------------------- 1 | ######################## 2 | #Control file for GOMC_GEMC_NVT 3 | ######################## 4 | 5 | ############################################################################ 6 | # ========-------------------- INPUT --------------------------=========== 7 | ############################################################################ 8 | 9 | ######################### 10 | # enable, step (DO NOT MODIFY or the hybrid simulation and combine files may not work) 11 | ######################### 12 | Restart restart_true_or_false 13 | 14 | Checkpoint Restart_Checkpoint_file 15 | #################################### 16 | # kind {RESTART, RANDOM, INTSEED} (DO NOT MODIFY or the hybrid simulation and combine files may not work) 17 | #################################### 18 | PRNG RANDOM 19 | 20 | #################################### 21 | # FORCE FIELD (DO NOT MODIFY or the hybrid simulation and combine files may not work) 22 | #################################### 23 | ParaTypeCHARMM true 24 | 25 | all_parameter_files 26 | #################################### 27 | # INPUT PDB FILES (DO NOT MODIFY or the hybrid simulation and combine files may not work) 28 | #################################### 29 | Coordinates 0 pdb_file_box_0_file 30 | Coordinates 1 pdb_file_box_1_file 31 | 32 | #################################### 33 | # INPUT PSF FILES (DO NOT MODIFY or the hybrid simulation and combine files may not work) 34 | #################################### 35 | Structure 0 psf_file_box_0_file 36 | Structure 1 psf_file_box_1_file 37 | 38 | #################################### 39 | # INPUT BINARY coodinatd, XSC, velocity files (DO NOT MODIFY or the hybrid simulation and combine files may not work) 40 | #################################### 41 | 42 | binCoordinates 0 coor_box_0_file 43 | extendedSystem 0 xsc_box_0_file 44 | binVelocities 0 vel_box_0_file 45 | 46 | binCoordinates 1 coor_box_1_file 47 | extendedSystem 1 xsc_box_1_file 48 | binVelocities 1 vel_box_1_file 49 | 50 | 51 | 52 | ############################################################################ 53 | # =======--------------------- SYSTEM --------------------------=========== 54 | ############################################################################ 55 | ################################## 56 | # GEMC TYPE (DEFULT IS NVT_GEMC) (DO NOT MODIFY or the hybrid simulation and combine files may not work) and Temp 57 | ################################## 58 | GEMC NVT 59 | Temperature System_temp_set 60 | 61 | ############################# 62 | # SIMULATION CONDITION 63 | ############################# 64 | Potential SWITCH 65 | Rswitch 10.0 66 | LRC false 67 | Rcut 12 68 | RcutLow 1.0 69 | Exclude 1-3 70 | 1-4scaling 1.0 71 | 72 | 73 | ############################# 74 | # ELECTROSTATIC 75 | ############################# 76 | Ewald true 77 | ElectroStatic true 78 | CachedFourier false 79 | Tolerance 0.00001 80 | 81 | 82 | ############################### 83 | # PRESSURE CALCULATION (DO NOT MODIFY or the hybrid simulation and combine files may not work) 84 | ################################ 85 | PressureCalc true GOMC_console_BLKavg_Hist_Steps 86 | 87 | ################################ 88 | # STEPS (DO NOT MODIFY or the hybrid simulation and combine files may not work) 89 | ################################ 90 | InitStep 0 91 | RunSteps GOMC_Run_Steps 92 | EqSteps GOMC_Equilb_Steps 93 | AdjSteps GOMC_Adj_Steps 94 | 95 | 96 | 97 | ################################ 98 | # MOVE FREQUENCY 99 | ################################ 100 | 101 | VolFreq 0.01 102 | SwapFreq 0.99 103 | DisFreq 0.00 104 | RotFreq 0.00 105 | RegrowthFreq 0.00 106 | IntraSwapFreq 0.00 107 | 108 | 109 | ################################ 110 | # BOX DIMENSION #, X, Y, Z (DO NOT MODIFY or the hybrid simulation and combine files may not work) 111 | ################################ 112 | CellBasisVector1 0 x_dim_box_0 0.00 0.00 113 | CellBasisVector2 0 0.00 y_dim_box_0 0.00 114 | CellBasisVector3 0 0.00 0.00 z_dim_box_0 115 | 116 | CellBasisVector1 1 x_dim_box_1 0.00 0.00 117 | CellBasisVector2 1 0.00 y_dim_box_1 0.00 118 | CellBasisVector3 1 0.00 0.00 z_dim_box_1 119 | 120 | 121 | 122 | ############################## 123 | # CBMC TRIALS 124 | ############################## 125 | CBMC_First 16 126 | CBMC_Nth 8 127 | CBMC_Ang 50 128 | CBMC_Dih 50 129 | 130 | 131 | ############################################################################ 132 | # =======-------------------- OUTPUT (DO NOT MODIFY or the hybrid simulation and combine files may not work) --------------------------=========== 133 | ############################################################################ 134 | 135 | ########################## 136 | # statistics filename add (DO NOT MODIFY or the hybrid simulation and combine files may not work) 137 | ########################## 138 | OutputName Output_data 139 | 140 | ##################################### 141 | # enable, frequency (DO NOT MODIFY or the hybrid simulation and combine files may not work) 142 | ##################################### 143 | RestartFreq true GOMC_RST_Coor_CKpoint_Steps 144 | CheckpointFreq true GOMC_RST_Coor_CKpoint_Steps 145 | CoordinatesFreq false GOMC_RST_Coor_CKpoint_Steps 146 | ConsoleFreq true GOMC_console_BLKavg_Hist_Steps 147 | BlockAverageFreq true GOMC_console_BLKavg_Hist_Steps 148 | HistogramFreq true GOMC_console_BLKavg_Hist_Steps 149 | DCDFreq true GOMC_RST_Coor_CKpoint_Steps 150 | 151 | ################################ 152 | # OutHistSettings (DO NOT MODIFY or the hybrid simulation and combine files may not work) 153 | ################################ 154 | DistName dis 155 | HistName his 156 | RunNumber 1 157 | RunLetter a 158 | SampleFreq GOMC_Hist_sample_Steps 159 | 160 | ################################## 161 | # enable: blk avg., fluct. (DO NOT MODIFY or the hybrid simulation and combine files may not work) 162 | ################################## 163 | OutEnergy true true 164 | OutPressure true true 165 | OutMolNum true true 166 | OutDensity true true 167 | OutVolume true true 168 | OutSurfaceTension false false 169 | -------------------------------------------------------------------------------- /required_data/config_files/GOMC_NPT.conf: -------------------------------------------------------------------------------- 1 | ######################## 2 | #Control file for GOMC_NPT 3 | ######################## 4 | 5 | ############################################################################ 6 | # ========-------------------- INPUT --------------------------=========== 7 | ############################################################################ 8 | 9 | ######################### 10 | # enable, step (DO NOT MODIFY or the hybrid simulation and combine files may not work) 11 | ######################### 12 | Restart restart_true_or_false 13 | 14 | Checkpoint Restart_Checkpoint_file 15 | #################################### 16 | # kind {RESTART, RANDOM, INTSEED} (DO NOT MODIFY or the hybrid simulation and combine files may not work) 17 | #################################### 18 | PRNG RANDOM 19 | 20 | #################################### 21 | # FORCE FIELD (DO NOT MODIFY or the hybrid simulation and combine files may not work) 22 | #################################### 23 | ParaTypeCHARMM true 24 | 25 | all_parameter_files 26 | #################################### 27 | # INPUT PDB FILES (DO NOT MODIFY or the hybrid simulation and combine files may not work) 28 | #################################### 29 | Coordinates 0 pdb_file_box_0_file 30 | 31 | #################################### 32 | # INPUT PSF FILES (DO NOT MODIFY or the hybrid simulation and combine files may not work) 33 | #################################### 34 | Structure 0 psf_file_box_0_file 35 | 36 | #################################### 37 | # INPUT BINARY coodinatd, XSC, velocity files (DO NOT MODIFY or the hybrid simulation and combine files may not work) 38 | #################################### 39 | 40 | binCoordinates 0 coor_box_0_file 41 | extendedSystem 0 xsc_box_0_file 42 | binVelocities 0 vel_box_0_file 43 | 44 | 45 | 46 | 47 | ############################################################################ 48 | # =======--------------------- SYSTEM --------------------------=========== 49 | ############################################################################ 50 | ################################## 51 | # Pressure and Temp (DO NOT MODIFY or the hybrid simulation and combine files may not work) 52 | ################################## 53 | Pressure System_press_set 54 | Temperature System_temp_set 55 | 56 | ############################# 57 | # SIMULATION CONDITION 58 | ############################# 59 | Potential SWITCH 60 | Rswitch 10.0 61 | LRC false 62 | Rcut 12 63 | RcutLow 1.0 64 | Exclude 1-3 65 | 1-4scaling 1.0 66 | 67 | 68 | ############################# 69 | # ELECTROSTATIC 70 | ############################# 71 | Ewald true 72 | ElectroStatic true 73 | CachedFourier false 74 | Tolerance 0.00001 75 | 76 | 77 | ############################### 78 | # PRESSURE CALCULATION (DO NOT MODIFY or the hybrid simulation and combine files may not work) 79 | ################################ 80 | PressureCalc true GOMC_console_BLKavg_Hist_Steps 81 | 82 | ################################ 83 | # STEPS (DO NOT MODIFY or the hybrid simulation and combine files may not work) 84 | ################################ 85 | InitStep 0 86 | RunSteps GOMC_Run_Steps 87 | EqSteps GOMC_Equilb_Steps 88 | AdjSteps GOMC_Adj_Steps 89 | 90 | 91 | 92 | ################################ 93 | # MOVE FREQUENCY 94 | ################################ 95 | 96 | VolFreq 0.01 97 | IntraSwapFreq 0.99 98 | DisFreq 0.00 99 | RotFreq 0.00 100 | RegrowthFreq 0.00 101 | 102 | 103 | 104 | ################################ 105 | # BOX DIMENSION #, X, Y, Z (DO NOT MODIFY or the hybrid simulation and combine files may not work) 106 | ################################ 107 | CellBasisVector1 0 x_dim_box_0 0.00 0.00 108 | CellBasisVector2 0 0.00 y_dim_box_0 0.00 109 | CellBasisVector3 0 0.00 0.00 z_dim_box_0 110 | 111 | 112 | 113 | 114 | ############################## 115 | # CBMC TRIALS 116 | ############################## 117 | CBMC_First 16 118 | CBMC_Nth 8 119 | CBMC_Ang 50 120 | CBMC_Dih 50 121 | 122 | 123 | ############################################################################ 124 | # =======-------------------- OUTPUT (DO NOT MODIFY or the hybrid simulation and combine files may not work) --------------------------=========== 125 | ############################################################################ 126 | 127 | ########################## 128 | # statistics filename add (DO NOT MODIFY or the hybrid simulation and combine files may not work) 129 | ########################## 130 | OutputName Output_data 131 | 132 | ##################################### 133 | # enable, frequency (DO NOT MODIFY or the hybrid simulation and combine files may not work) 134 | ##################################### 135 | RestartFreq true GOMC_RST_Coor_CKpoint_Steps 136 | CheckpointFreq true GOMC_RST_Coor_CKpoint_Steps 137 | CoordinatesFreq false GOMC_RST_Coor_CKpoint_Steps 138 | ConsoleFreq true GOMC_console_BLKavg_Hist_Steps 139 | BlockAverageFreq true GOMC_console_BLKavg_Hist_Steps 140 | HistogramFreq true GOMC_console_BLKavg_Hist_Steps 141 | DCDFreq true GOMC_RST_Coor_CKpoint_Steps 142 | 143 | ################################ 144 | # OutHistSettings (DO NOT MODIFY or the hybrid simulation and combine files may not work) 145 | ################################ 146 | DistName dis 147 | HistName his 148 | RunNumber 1 149 | RunLetter a 150 | SampleFreq GOMC_Hist_sample_Steps 151 | 152 | ################################## 153 | # enable: blk avg., fluct. (DO NOT MODIFY or the hybrid simulation and combine files may not work) 154 | ################################## 155 | OutEnergy true true 156 | OutPressure true true 157 | OutMolNum true true 158 | OutDensity true true 159 | OutVolume true true 160 | OutSurfaceTension false false 161 | -------------------------------------------------------------------------------- /required_data/config_files/GOMC_NVT.conf: -------------------------------------------------------------------------------- 1 | ######################## 2 | #Control file for GOMC_NVT 3 | ######################## 4 | 5 | ############################################################################ 6 | # ========-------------------- INPUT --------------------------=========== 7 | ############################################################################ 8 | 9 | ######################### 10 | # enable, step (DO NOT MODIFY or the hybrid simulation and combine files may not work) 11 | ######################### 12 | Restart restart_true_or_false 13 | 14 | Checkpoint Restart_Checkpoint_file 15 | #################################### 16 | # kind {RESTART, RANDOM, INTSEED} (DO NOT MODIFY or the hybrid simulation and combine files may not work) 17 | #################################### 18 | PRNG RANDOM 19 | 20 | #################################### 21 | # FORCE FIELD (DO NOT MODIFY or the hybrid simulation and combine files may not work) 22 | #################################### 23 | ParaTypeCHARMM true 24 | 25 | all_parameter_files 26 | #################################### 27 | # INPUT PDB FILES (DO NOT MODIFY or the hybrid simulation and combine files may not work) 28 | #################################### 29 | Coordinates 0 pdb_file_box_0_file 30 | 31 | #################################### 32 | # INPUT PSF FILES (DO NOT MODIFY or the hybrid simulation and combine files may not work) 33 | #################################### 34 | Structure 0 psf_file_box_0_file 35 | 36 | #################################### 37 | # INPUT BINARY coodinatd, XSC, velocity files (DO NOT MODIFY or the hybrid simulation and combine files may not work) 38 | #################################### 39 | 40 | binCoordinates 0 coor_box_0_file 41 | extendedSystem 0 xsc_box_0_file 42 | binVelocities 0 vel_box_0_file 43 | 44 | 45 | 46 | ############################################################################ 47 | # =======--------------------- SYSTEM --------------------------=========== 48 | ############################################################################ 49 | 50 | ################################## 51 | # Temp (DO NOT MODIFY or the hybrid simulation and combine files may not work) 52 | ################################## 53 | Temperature System_temp_set 54 | 55 | ############################# 56 | # SIMULATION CONDITION 57 | ############################# 58 | Potential SWITCH 59 | Rswitch 10.0 60 | LRC false 61 | Rcut 12 62 | RcutLow 1.0 63 | Exclude 1-3 64 | 1-4scaling 1.0 65 | 66 | 67 | ############################# 68 | # ELECTROSTATIC 69 | ############################# 70 | Ewald true 71 | ElectroStatic true 72 | CachedFourier false 73 | Tolerance 0.00001 74 | 75 | 76 | ############################### 77 | # PRESSURE CALCULATION (DO NOT MODIFY or the hybrid simulation and combine files may not work) 78 | ################################ 79 | PressureCalc true GOMC_console_BLKavg_Hist_Steps 80 | 81 | ################################ 82 | # STEPS (DO NOT MODIFY or the hybrid simulation and combine files may not work) 83 | ################################ 84 | InitStep 0 85 | RunSteps GOMC_Run_Steps 86 | EqSteps GOMC_Equilb_Steps 87 | AdjSteps GOMC_Adj_Steps 88 | 89 | 90 | 91 | ################################ 92 | # MOVE FREQUENCY (DO NOT MODIFY or the hybrid simulation and combine files may not work) 93 | ################################ 94 | 95 | IntraSwapFreq 1.000 96 | DisFreq 0.000 97 | RotFreq 0.000 98 | RegrowthFreq 0.000 99 | 100 | ################################ 101 | # BOX DIMENSION #, X, Y, Z (DO NOT MODIFY or the hybrid simulation and combine files may not work) 102 | ################################ 103 | CellBasisVector1 0 x_dim_box_0 0.00 0.00 104 | CellBasisVector2 0 0.00 y_dim_box_0 0.00 105 | CellBasisVector3 0 0.00 0.00 z_dim_box_0 106 | 107 | 108 | 109 | 110 | ############################## 111 | # CBMC TRIALS 112 | ############################## 113 | CBMC_First 16 114 | CBMC_Nth 8 115 | CBMC_Ang 50 116 | CBMC_Dih 50 117 | 118 | 119 | ############################################################################ 120 | # =======-------------------- OUTPUT (DO NOT MODIFY or the hybrid simulation and combine files may not work) --------------------------=========== 121 | ############################################################################ 122 | 123 | ########################## 124 | # statistics filename add (DO NOT MODIFY or the hybrid simulation and combine files may not work) 125 | ########################## 126 | OutputName Output_data 127 | 128 | ##################################### 129 | # enable, frequency (DO NOT MODIFY or the hybrid simulation and combine files may not work) 130 | ##################################### 131 | RestartFreq true GOMC_RST_Coor_CKpoint_Steps 132 | CheckpointFreq true GOMC_RST_Coor_CKpoint_Steps 133 | CoordinatesFreq false GOMC_RST_Coor_CKpoint_Steps 134 | ConsoleFreq true GOMC_console_BLKavg_Hist_Steps 135 | BlockAverageFreq true GOMC_console_BLKavg_Hist_Steps 136 | HistogramFreq true GOMC_console_BLKavg_Hist_Steps 137 | DCDFreq true GOMC_RST_Coor_CKpoint_Steps 138 | 139 | ################################ 140 | # OutHistSettings (DO NOT MODIFY or the hybrid simulation and combine files may not work) 141 | ################################ 142 | DistName dis 143 | HistName his 144 | RunNumber 1 145 | RunLetter a 146 | SampleFreq GOMC_Hist_sample_Steps 147 | 148 | ################################## 149 | # enable: blk avg., fluct. (DO NOT MODIFY or the hybrid simulation and combine files may not work) 150 | ################################## 151 | OutEnergy true true 152 | OutPressure true true 153 | OutMolNum true true 154 | OutDensity true true 155 | OutVolume true true 156 | OutSurfaceTension false false 157 | -------------------------------------------------------------------------------- /required_data/config_files/NAMD.conf: -------------------------------------------------------------------------------- 1 | ############################################################# 2 | ## JOB DESCRIPTION ## 3 | ############################################################# 4 | 5 | # Minimization and Equilibration of 6 | # Ubiquitin in a Water Box 7 | 8 | # (DO NOT MODIFY anything but the Force-Field Parameters or Integrator Parameters 9 | # or the hybrid simulation and combine files may not work) 10 | ############################################################# 11 | ## PYTHON CODE INPUT PARMETERS ONLY (DO NOT MODIFY or the hybrid simulation and combine files may not work) ## 12 | ############################################################# 13 | 14 | all_parameter_files 15 | 16 | coordinates pdb_box_file 17 | structure psf_box_file 18 | 19 | set X_DIM_box x_dim_box 20 | set Y_DIM_box y_dim_box 21 | set Z_DIM_box z_dim_box 22 | 23 | set X_ORIGIN_box x_origin_box 24 | set Y_ORIGIN_box y_origin_box 25 | set Z_ORIGIN_box z_origin_box 26 | 27 | set PME_Grid_Size_X X_PME_GRID_DIM 28 | set PME_Grid_Size_Y Y_PME_GRID_DIM 29 | set PME_Grid_Size_Z Z_PME_GRID_DIM 30 | 31 | set NAMD_RUN_STEPS NAMD_Run_Steps 32 | set NAMD_MINIMIZE NAMD_Minimize 33 | 34 | set set_temperature System_temp_set 35 | 36 | 37 | set RESTART_STATUS Bool_restart 38 | 39 | if {${RESTART_STATUS}} { 40 | set COOR_file coor_file 41 | set XSC_file xsc_file 42 | set VEL_file vel_file 43 | } else { 44 | 45 | } 46 | 47 | firsttimestep current_step 48 | set outputname namdOut 49 | 50 | ############################################################# 51 | ## Add fix or restrain input here (below). This may only work with the relative path the fix or restrain pdb files ## 52 | ############################################################# 53 | 54 | 55 | ############################################################# 56 | ## ADJUSTABLE PARAMETERS SIMULATION PARAMETERS, WITH CAUTION ## 57 | ############################################################# 58 | 59 | # Input 60 | paraTypeCharmm on 61 | 62 | 63 | # Force-Field Parameters 64 | exclude scaled1-4 65 | 1-4scaling 1.0 66 | cutoff 12.0 67 | switching on 68 | switchdist 10.0 69 | pairlistdist 16.0 70 | margin 3.0 71 | 72 | # Integrator Parameters 73 | timestep 2.0 ;# 2fs/step 74 | rigidBonds all ;# needed for 2fs steps 75 | nonbondedFreq 1 76 | fullElectFrequency 2 77 | stepspercycle 10 78 | PMETolerance 0.00001 79 | 80 | 81 | # PME (for full-system periodic electrostatics) 82 | PME yes 83 | #PMEGridSpacing 1.0 84 | 85 | 86 | ############################################################# 87 | ## FIXED NVT SIMULATION (VOLUME CHANGES HANDLED IN GOMC) and AUTO-BOX SIZING: 88 | ## (ONLY run NAMD in the NVT ensemble, as running NAMD in the NPT ensemble will cause errors 89 | ## in the box positioning since NAMD and GOMC have different box centering algorithms 90 | ## when centering the box during box size changes. ) 91 | ## (DO NOT MODIFY or the hybrid simulation and combine files may not work) ## 92 | ############################################################# 93 | 94 | #manual grid definition 95 | PMEGridSizeX ${PME_Grid_Size_X} 96 | PMEGridSizeY ${PME_Grid_Size_Y} 97 | PMEGridSizeZ ${PME_Grid_Size_Z} 98 | 99 | 100 | # Constant Temperature Control 101 | langevin on ;# do langevin dynamics 102 | langevinDamping 1 ;# damping coefficient (gamma) of 1/ps 103 | langevinTemp $set_temperature 104 | langevinHydrogen off ;# don't couple langevin bath to hydrogens 105 | 106 | 107 | # Constant Pressure Control (variable volume) 108 | useGroupPressure yes ;# needed for rigidBonds 109 | useFlexibleCell no 110 | useConstantArea no 111 | 112 | langevinPiston off 113 | #langevinPistonTarget System_press_set ;# in bar -> 1 atm 114 | #langevinPistonPeriod 100.0 115 | #langevinPistonDecay 50.0 116 | #langevinPistonTemp $set_temperature 117 | 118 | 119 | wrapAll on 120 | 121 | if {${RESTART_STATUS}} { 122 | binCoordinates ${COOR_file} 123 | extendedSystem ${XSC_file} 124 | binvelocities ${VEL_file} 125 | 126 | } else { 127 | # set the temp for the intial simulation 128 | temperature $set_temperature 129 | 130 | # Periodic Boundary Conditions 131 | CellBasisVector1 ${X_DIM_box} 0.00 0.00 132 | CellBasisVector2 0.00 ${Y_DIM_box} 0.00 133 | CellBasisVector3 0.00 0.00 ${Z_DIM_box} 134 | cellOrigin ${X_ORIGIN_box} ${Y_ORIGIN_box} ${Z_ORIGIN_box} 135 | } 136 | 137 | 138 | # Output 139 | outputName $outputname 140 | 141 | restartfreq NAMD_RST_DCD_XST_Steps ;# 500steps = every 1ps 142 | dcdfreq NAMD_RST_DCD_XST_Steps 143 | xstFreq NAMD_RST_DCD_XST_Steps 144 | outputEnergies NAMD_console_BLKavg_E_and_P_Steps 145 | outputPressure NAMD_console_BLKavg_E_and_P_Steps 146 | 147 | 148 | ############################################################# 149 | ## EXTRA PARAMETERS ## 150 | ############################################################# 151 | 152 | 153 | ############################################################# 154 | ## EXECUTION SCRIPT (DO NOT MODIFY or the hybrid simulation and combine files may not work) ## 155 | ############################################################# 156 | 157 | # Minimization 158 | if {${RESTART_STATUS}} { 159 | 160 | } else { 161 | minimize $NAMD_MINIMIZE 162 | } 163 | 164 | 165 | 166 | run $NAMD_RUN_STEPS 167 | -------------------------------------------------------------------------------- /required_data/equilb_box_298K/GOMC_TIPS3P_FF copy.inp: -------------------------------------------------------------------------------- 1 | * TIPS3P_box_0 and TIPS3P_reservoir_box_1 - created by mBuild using the on 2021-02-27 15:50:47.100391 2 | * parameters from the {'TIP3': 'files/TIPS3P_bonded_Hs.xml', 'WAT': 'files/TIPS3P_bonded_Hs.xml'} force field(s) via MoSDef 3 | * 1-4 coulombic scaling = {'TIP3': 1.0, 'WAT': 1.0}, and 1-4 LJ scaling = {'TIP3': 1.0, 'WAT': 1.0} 4 | 5 | * 19275 atoms 6 | * 12850 bonds 7 | * 6425 angles 8 | * 0 dihedrals 9 | * 0 impropers 10 | 11 | * 4 atom types 12 | * 2 bond types 13 | * 2 angle types 14 | 15 | 16 | * masses 17 | 18 | ! atom_types mass atomTypeForceFieldName_ResidueName (i.e., atoms_type_per_utilized_FF) 19 | * O 15.999430 ! TIPS3P_O_TIP3 20 | * H 1.007947 ! TIPS3P_H_TIP3 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | BONDS * harmonic 31 | ! 32 | !V(bond) = Kb(b - b0)**2 33 | ! 34 | !Kb: kcal/mole/A**2 35 | !b0: A 36 | !Kb (kcal/mol) = Kb_K (K) * Boltz. const.; 37 | ! 38 | !atom_types Kb b0 39 | H O 999999999999 0.9572 40 | 41 | ANGLES * harmonic 42 | ! 43 | !V(angle) = Ktheta(Theta - Theta0)**2 44 | ! 45 | !Ktheta: kcal/mole/rad**2 46 | !Theta0: degrees 47 | ! 48 | ! Ktheta (kcal/mol) = Ktheta_K (K) * Boltz. const. 49 | ! 50 | ! atom_types Ktheta Theta0 51 | H O H 999999999999 104.52000 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | NONBONDED 60 | ! 61 | !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] 62 | ! 63 | !atype ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 atom_type_per_utilized_FF 64 | C 0.00 -0.152100000 1.76820000000 0.00 -0.152100000 1.76820000000 ! TIPS3P_O_TIP3 TIPS3P_O_TIP3 65 | A 0.00 -0.046000000 0.22450000000 0.00 -0.046000000 0.22450000000 ! TIPS3P_H_TIP3 TIPS3P_H_TIP3 66 | D 0.00 -0.152100000 1.76820000000 0.00 -0.152100000 1.76820000000 ! TIPS3P_O_WAT TIPS3P_O_WAT 67 | B 0.00 -0.046000000 0.22450000000 0.00 -0.046000000 0.22450000000 ! TIPS3P_H_WAT TIPS3P_H_WAT 68 | 69 | END 70 | -------------------------------------------------------------------------------- /required_data/equilb_box_298K/GOMC_TIPS3P_FF.inp: -------------------------------------------------------------------------------- 1 | * TIPS3P_box_0 and TIPS3P_reservoir_box_1 - created by mBuild using the on 2021-02-27 15:50:47.100391 2 | * parameters from the {'TIP3': 'files/TIPS3P_bonded_Hs.xml', 'WAT': 'files/TIPS3P_bonded_Hs.xml'} force field(s) via MoSDef 3 | * 1-4 coulombic scaling = {'TIP3': 1.0, 'WAT': 1.0}, and 1-4 LJ scaling = {'TIP3': 1.0, 'WAT': 1.0} 4 | 5 | * 19275 atoms 6 | * 12850 bonds 7 | * 6425 angles 8 | * 0 dihedrals 9 | * 0 impropers 10 | 11 | * 4 atom types 12 | * 2 bond types 13 | * 2 angle types 14 | 15 | 16 | * masses 17 | 18 | ! atom_types mass atomTypeForceFieldName_ResidueName (i.e., atoms_type_per_utilized_FF) 19 | * C 15.999430 ! TIPS3P_O_TIP3 20 | * A 1.007947 ! TIPS3P_H_TIP3 21 | * D 15.999430 ! TIPS3P_O_WAT 22 | * B 1.007947 ! TIPS3P_H_WAT 23 | 24 | BONDS * harmonic 25 | ! 26 | !V(bond) = Kb(b - b0)**2 27 | ! 28 | !Kb: kcal/mole/A**2 29 | !b0: A 30 | !Kb (kcal/mol) = Kb_K (K) * Boltz. const.; (9999999999 if no stretching) 31 | ! 32 | !atom_types Kb b0 atoms_types_per_utilized_FF 33 | B D 999999999999 0.9572 ! TIPS3P_H_WAT TIPS3P_O_WAT 34 | A C 999999999999 0.9572 ! TIPS3P_H_TIP3 TIPS3P_O_TIP3 35 | 36 | ANGLES * harmonic 37 | ! 38 | !V(angle) = Ktheta(Theta - Theta0)**2 39 | ! 40 | !Ktheta: kcal/mole/rad**2 41 | !Theta0: degrees 42 | ! 43 | ! Ktheta (kcal/mol) = Ktheta_K (K) * Boltz. const. 44 | ! 45 | !atom_types Ktheta Theta0 atoms_types_per_utilized_FF 46 | A C A 999999999999 104.52000 ! TIPS3P_H_TIP3 TIPS3P_O_TIP3 TIPS3P_H_TIP3 47 | B D B 999999999999 104.52000 ! TIPS3P_H_WAT TIPS3P_O_WAT TIPS3P_H_WAT 48 | 49 | NONBONDED 50 | ! 51 | !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] 52 | ! 53 | !atype ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 atom_type_per_utilized_FF 54 | C 0.00 -0.152100000 1.76820000000 0.00 -0.152100000 1.76820000000 ! TIPS3P_O_TIP3 TIPS3P_O_TIP3 55 | A 0.00 -0.046000000 0.22450000000 0.00 -0.046000000 0.22450000000 ! TIPS3P_H_TIP3 TIPS3P_H_TIP3 56 | D 0.00 -0.152100000 1.76820000000 0.00 -0.152100000 1.76820000000 ! TIPS3P_O_WAT TIPS3P_O_WAT 57 | B 0.00 -0.046000000 0.22450000000 0.00 -0.046000000 0.22450000000 ! TIPS3P_H_WAT TIPS3P_H_WAT 58 | 59 | END 60 | -------------------------------------------------------------------------------- /required_data/equilb_box_298K/NAMD_TIPS3P_FF.inp: -------------------------------------------------------------------------------- 1 | * TIPS3P_box_0 and TIPS3P_reservoir_box_1 - created by mBuild using the on 2021-02-27 15:51:14.293116 2 | * parameters from the {'TIP3': 'files/TIPS3P_bonded_Hs.xml', 'WAT': 'files/TIPS3P_bonded_Hs.xml'} force field(s) via MoSDef 3 | * 1-4 coulombic scaling = {'TIP3': 1.0, 'WAT': 1.0}, and 1-4 LJ scaling = {'TIP3': 1.0, 'WAT': 1.0} 4 | 5 | * 19275 atoms 6 | * 12850 bonds 7 | * 6425 angles 8 | * 0 dihedrals 9 | * 0 impropers 10 | 11 | * 4 atom types 12 | * 2 bond types 13 | * 2 angle types 14 | 15 | 16 | * masses 17 | 18 | ! atom_types mass atomTypeForceFieldName_ResidueName (i.e., atoms_type_per_utilized_FF) 19 | * C 15.999430 ! TIPS3P_O_TIP3 20 | * A 1.007947 ! TIPS3P_H_TIP3 21 | * D 15.999430 ! TIPS3P_O_WAT 22 | * B 1.007947 ! TIPS3P_H_WAT 23 | 24 | BONDS * harmonic 25 | ! 26 | !V(bond) = Kb(b - b0)**2 27 | ! 28 | !Kb: kcal/mole/A**2 29 | !b0: A 30 | !Kb (kcal/mol) = Kb_K (K) * Boltz. const.; (9999999999 if no stretching) 31 | ! 32 | !atom_types Kb b0 atoms_types_per_utilized_FF 33 | B D 450.0 0.9572 ! TIPS3P_H_WAT TIPS3P_O_WAT 34 | A C 450.0 0.9572 ! TIPS3P_H_TIP3 TIPS3P_O_TIP3 35 | 36 | ANGLES * harmonic 37 | ! 38 | !V(angle) = Ktheta(Theta - Theta0)**2 39 | ! 40 | !Ktheta: kcal/mole/rad**2 41 | !Theta0: degrees 42 | ! 43 | ! Ktheta (kcal/mol) = Ktheta_K (K) * Boltz. const. 44 | ! 45 | !atom_types Ktheta Theta0 atoms_types_per_utilized_FF 46 | A C A 55.0 104.52000 ! TIPS3P_H_TIP3 TIPS3P_O_TIP3 TIPS3P_H_TIP3 47 | B D B 55.0 104.52000 ! TIPS3P_H_WAT TIPS3P_O_WAT TIPS3P_H_WAT 48 | 49 | NONBONDED 50 | ! 51 | !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] 52 | ! 53 | !atype ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 atom_type_per_utilized_FF 54 | C 0.00 -0.152100000 1.76820000000 0.00 -0.152100000 1.76820000000 ! TIPS3P_O_TIP3 TIPS3P_O_TIP3 55 | A 0.00 -0.046000000 0.22450000000 0.00 -0.046000000 0.22450000000 ! TIPS3P_H_TIP3 TIPS3P_H_TIP3 56 | D 0.00 -0.152100000 1.76820000000 0.00 -0.152100000 1.76820000000 ! TIPS3P_O_WAT TIPS3P_O_WAT 57 | B 0.00 -0.046000000 0.22450000000 0.00 -0.046000000 0.22450000000 ! TIPS3P_H_WAT TIPS3P_H_WAT 58 | 59 | END 60 | -------------------------------------------------------------------------------- /user_input_NAMD_GOMC.json: -------------------------------------------------------------------------------- 1 | {"total_cycles_namd_gomc_sims": 10, 2 | "starting_at_cycle_namd_gomc_sims": 0, 3 | "gomc_use_CPU_or_GPU": "GPU" , 4 | "simulation_type": "GCMC", 5 | "only_use_box_0_for_namd_for_gemc": false, 6 | "no_core_box_0": 8, 7 | "no_core_box_1" : 0, 8 | "simulation_temp_k": 298, 9 | "simulation_pressure_bar": 1.01325, 10 | "GCMC_ChemPot_or_Fugacity": "ChemPot", 11 | "GCMC_ChemPot_or_Fugacity_dict": {"TIP3": -1000, "WAT": -2000}, 12 | "namd_minimize_mult_scalar": 1, 13 | "namd_run_steps": 500, 14 | "gomc_run_steps": 500, 15 | "set_dims_box_0_list": null, 16 | "set_dims_box_1_list": null, 17 | "set_angle_box_0_list": null, 18 | "set_angle_box_1_list": null, 19 | "starting_ff_file_list_gomc": ["required_data/equilb_box_298K/GOMC_TIPS3P_FF.inp"], 20 | "starting_ff_file_list_namd": ["required_data/equilb_box_298K/NAMD_TIPS3P_FF.inp"], 21 | "starting_pdb_box_0_file": "required_data/equilb_box_298K/TIPS3P_box_0.pdb", 22 | "starting_psf_box_0_file": "required_data/equilb_box_298K/TIPS3P_box_0.psf", 23 | "starting_pdb_box_1_file": "required_data/equilb_box_298K/TIPS3P_reservoir_box_1.pdb", 24 | "starting_psf_box_1_file": "required_data/equilb_box_298K/TIPS3P_reservoir_box_1.psf", 25 | "namd2_bin_directory": "required_data/bin/NAMD_CPU", 26 | "gomc_bin_directory": "required_data/bin"} 27 | -------------------------------------------------------------------------------- /user_input_combine_data_NAMD_GOMC.json: -------------------------------------------------------------------------------- 1 | {"simulation_type": "GCMC", 2 | "only_use_box_0_for_namd_for_gemc": true, 3 | "simulation_engine_options": "Hybrid", 4 | "gomc_or_namd_only_log_filename": "out.dat", 5 | "combine_namd_dcd_file": true, 6 | "combine_gomc_dcd_file": true, 7 | "combine_dcd_files_cycle_freq": 1, 8 | "get_initial_gomc_dcd": true, 9 | "rel_path_to_combine_binary_catdcd": "required_data/bin/catdcd-4.0b/LINUXAMD64/bin/catdcd4.0/catdcd"} 10 | --------------------------------------------------------------------------------