├── .github └── workflows │ └── CI.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── CITATION.cff ├── Dockerfile ├── LICENSE.rst ├── MANIFEST.in ├── README.md ├── codecov.yml ├── devtools └── docker-entrypoint.sh ├── docs ├── Makefile ├── _images │ └── mosdef_gomc_license ├── conf.py ├── environment_docs.yml ├── getting_started │ ├── installation │ │ └── installation.rst │ └── quick_start │ │ ├── build_a_system_and_write_all_files.rst │ │ ├── gomc_examples_repository.rst │ │ └── quick_start.rst ├── index.rst ├── make.bat ├── overview │ ├── general_info.rst │ └── supported_chemical_systems.rst ├── reference │ ├── citing_mosdef_gomc_python.rst │ ├── credits.rst │ ├── mosdef_gomc_paper.bib │ ├── mosdef_gomc_paper.ris │ ├── mosdef_gomc_python.bib │ ├── mosdef_gomc_python.ris │ ├── mosdef_gomc_zenodo.bib │ ├── mosdef_gomc_zenodo.ris │ ├── units.rst │ └── user_notices.rst ├── requirements.txt └── topic_guides │ ├── data_structures.rst │ └── load_data.rst ├── environment.yml ├── mosdef_gomc ├── __init__.py ├── formats │ ├── __init__.py │ ├── charmm_writer.py │ ├── gmso_charmm_writer.py │ ├── gmso_gomc_conf_writer.py │ └── gomc_conf_writer.py ├── tests │ ├── __init__.py │ ├── base_test.py │ ├── test_gmso_charmm_writer.py │ ├── test_gmso_equation_compare.py │ ├── test_gmso_gomc_conf_writer.py │ └── test_gmso_specific_ff_to_residue.py └── utils │ ├── __init__.py │ ├── conversion.py │ ├── files │ ├── 2_ethane.mol2 │ ├── Charmm_writer_testing_only_zeolite.xml │ ├── ETV_triclinic.cif │ ├── amber_aa_butane_CT_CT_CT_CT_with_fake_improper_gmso.xml │ ├── benzene_GAFF.xml │ ├── benzene_aa.mol2 │ ├── benzene_and_alkane_branched_benzene_aa.xml │ ├── butane_aa.mol2 │ ├── charmm_mie_ff_file_test_single_bonds_angles_dihedrals_impropers_ua.xml │ ├── charmm_psf_6_char_atom_names_test_single_bonds_angles_dihedrals_impropers_ua.xml │ ├── charmm_psf_7_char_atom_names_test_single_bonds_angles_dihedrals_impropers_ua.xml │ ├── charmm_psf_test_single_bonds_angles_dihedrals_impropers_ua.xml │ ├── ethane_propane_ua_Mie_lorentz_combining.xml │ ├── ethane_propane_ua_bad_eqn_lorentz_combining.xml │ ├── ethane_propane_ua_lorentz_combining.xml │ ├── ethane_ua.mol2 │ ├── ethane_ua_mie.mol2 │ ├── ethyl_benzene_aa.mol2 │ ├── gmso_benzene_GAFF.xml │ ├── gmso_hexane_Exp6_eqn_times_2_periodic_dihedral_ua_K_energy.xml │ ├── gmso_hexane_Exp6_periodic_dihedral_ua_K_energy_units.xml │ ├── gmso_spce_water_LJ_eqn_times_2_one_for_nb_and_coul__lorentz_combining.xml │ ├── gmso_spce_water__geometric_combining.xml │ ├── gmso_spce_water__lorentz_combining.xml │ ├── gmso_spce_water__no_combining_rule.xml │ ├── gmso_spce_water_bad_charges__lorentz_combining.xml │ ├── gmso_spce_water_half_for_nb__half_coul__lorentz_combining.xml │ ├── gmso_spce_water_one_for_nb_and_coul__lorentz_combining.xml │ ├── gmso_spce_water_zero_for_nb__half_coul__lorentz_combining.xml │ ├── gmso_spce_water_zero_for_nb_and_coul__geometric_combining.xml │ ├── gmso_two_propanol_Mie_OPLS_dihedral_ua_K_energy_units.xml │ ├── gmso_two_propanol_Mie_RB_dihedral_ua_K_energy_units.xml │ ├── gmso_two_propanol_Mie_eqn_time_2_ua.xml │ ├── gmso_two_propanol_Mie_half_for_nb__half_coul.xml │ ├── gmso_two_propanol_Mie_m_not_equal_6_ua.xml │ ├── gmso_two_propanol_Mie_periodic_dihedral_ua_K_energy_units.xml │ ├── gmso_two_propanol_Mie_periodic_dihedral_ua_K_energy_units_diff_Mie_n.xml │ ├── gmso_two_propanol_Mie_periodic_dihedral_ua_K_energy_units_diff_eplison.xml │ ├── gmso_two_propanol_Mie_periodic_dihedral_ua_K_energy_units_diff_mass.xml │ ├── gmso_two_propanol_Mie_periodic_dihedral_ua_K_energy_units_diff_sigma.xml │ ├── gmso_two_propanol_Mie_periodic_dihedral_ua_dihedral_with_same_n_values.xml │ ├── gmso_two_propanol_Mie_periodic_improper_ua_K_energy_units.xml │ ├── gmso_two_propanol_Mie_periodic_impropers_ua.xml │ ├── gmso_two_propanol_Mie_ua.xml │ ├── gmso_two_propanol_OPLS_dihedrals_0_5_times_1_ua.xml │ ├── gmso_two_propanol_OPLS_dihedrals_0_5_times_2_ua.xml │ ├── gmso_two_propanol_OPLS_dihedrals_half_times_1_ua.xml │ ├── gmso_two_propanol_OPLS_dihedrals_half_times_2_ua.xml │ ├── gmso_two_propanol_RB_dihedrals_times_1_ua.xml │ ├── gmso_two_propanol_RB_dihedrals_times_2_ua.xml │ ├── gmso_two_propanol_RB_dihedrals_ua.xml │ ├── gmso_two_propanol_bad_form_angles_ua.xml │ ├── gmso_two_propanol_bad_form_bonds_ua.xml │ ├── gmso_two_propanol_bad_form_dihedrals_ua.xml │ ├── gmso_two_propanol_harmonic_dihedrals_ua.xml │ ├── gmso_two_propanol_harmonic_impropers_ua.xml │ ├── gmso_two_propanol_harmonic_impropers_ua_with_2_harmonics_in_2_diff_forms.xml │ ├── gmso_two_propanol_periodic_dihedrals_ua_all_bond_angles_dihedrals_k_times_1.xml │ ├── gmso_two_propanol_periodic_dihedrals_ua_all_bond_angles_dihedrals_k_times_half.xml │ ├── gmso_two_propanol_periodic_impropers_ua.xml │ ├── gmso_two_propanol_periodic_wildcard_dihedrals_ua.xml │ ├── gmso_two_propanol_periodic_wildcard_impropers_ua.xml │ ├── gmso_two_propanol_some_bonded_types_and_classes.xml │ ├── gmso_two_propanol_some_bonded_types_and_classes_different_way.xml │ ├── hexane_ua.mol2 │ ├── methyl_benzene_aa.mol2 │ ├── propane_ua.mol2 │ ├── psf_file_single_angle_test_ua.mol2 │ ├── psf_file_single_bond_test_ua.mol2 │ ├── psf_file_single_dihedral_test_ua.mol2 │ ├── psf_file_single_improper_test_ua.mol2 │ └── spce_coul_14_half__LJ_14_zero.xml │ ├── gmso_equation_compare.py │ ├── gmso_specific_ff_to_residue.py │ └── io.py ├── setup.cfg └── setup.py /.github/workflows/CI.yml: -------------------------------------------------------------------------------- 1 | name: CI 2 | 3 | # Controls when the workflow will run 4 | on: 5 | # Triggers the workflow on push or pull request events but only for the main branch 6 | push: 7 | branches: [ main ] 8 | pull_request: 9 | branches: [ main ] 10 | schedule: 11 | - cron: "0 0 * * *" 12 | 13 | # Allows you to run this workflow manually from the Actions tab 14 | workflow_dispatch: 15 | 16 | # A workflow run is made up of one or more jobs that can run sequentially or in parallel 17 | jobs: 18 | Mambaforge-pytest: 19 | name: Unit-Test (${{ matrix.os }}, Python ${{ matrix.python-version }}) 20 | runs-on: ${{ matrix.os }}-latest 21 | strategy: 22 | fail-fast: false 23 | matrix: 24 | python-version: ["3.10", "3.11"] 25 | os: ["ubuntu", "macos"] 26 | include: 27 | - os: ubuntu 28 | environment-file: environment.yml 29 | - os: macos 30 | environment-file: environment.yml 31 | steps: 32 | - uses: actions/checkout@v4 33 | - uses: conda-incubator/setup-miniconda@v3 34 | with: 35 | environment-file: ${{ matrix.environment-file }} 36 | miniforge-variant: ${{ matrix.miniforge-variant }} 37 | miniforge-version: ${{ matrix.miniforge-version }} 38 | python-version: ${{ matrix.python-version }} 39 | use-mamba: true 40 | 41 | - shell: bash -l {0} 42 | run: | 43 | pip install . 44 | 45 | - shell: bash -l {0} 46 | run: | 47 | python -m pytest -v --color yes mosdef_gomc/tests --cov 48 | coverage xml 49 | echo "tests finished" 50 | 51 | - name: Upload coverage reports to Codecov 52 | uses: codecov/codecov-action@v3 53 | 54 | docker: 55 | runs-on: 'ubuntu-latest' 56 | needs: Mambaforge-pytest 57 | name: 'Build Docker Image' 58 | if: github.event_name != 'pull_request' 59 | 60 | steps: 61 | - name: Set up Docker Buildx 62 | uses: docker/setup-buildx-action@v3 63 | 64 | - name: Login to DockerHub 65 | uses: docker/login-action@v3 66 | with: 67 | username: ${{ secrets.DOCKERHUB_USERNAME }} 68 | password: ${{ secrets.DOCKERHUB_PASSWORD }} 69 | 70 | - name: Get Tagged Version 71 | run: | 72 | echo "DOCKER_TAGS=${{ secrets.DOCKERHUB_USERNAME }}/mosdef-gomc:${GITHUB_REF_NAME}, ${{ secrets.DOCKERHUB_USERNAME }}/mosdef-gomc:stable" >> $GITHUB_ENV 73 | if: github.ref_type == 'tag' 74 | 75 | - name: Get Push Version 76 | run: | 77 | echo "DOCKER_TAGS=${{ secrets.DOCKERHUB_USERNAME }}/mosdef-gomc:${GITHUB_REF_NAME}, ${{ secrets.DOCKERHUB_USERNAME }}/mosdef-gomc:latest" >> $GITHUB_ENV 78 | if: github.ref_type == 'branch' 79 | 80 | - name: Docker Image Info 81 | run: | 82 | echo Docker Image tags: ${DOCKER_TAGS} 83 | 84 | - name: Build and Push 85 | uses: docker/build-push-action@v5 86 | with: 87 | push: true 88 | tags: ${{ env.DOCKER_TAGS }} 89 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | test-output.xml 2 | *.py[cod] 3 | *.ipynb_checkpoints 4 | .pymon 5 | 6 | # C extensions 7 | *.so 8 | 9 | # github 10 | **/.DS_Store 11 | 12 | # Packages 13 | *.egg 14 | *.egg-info 15 | dist 16 | build 17 | eggs 18 | parts 19 | bin 20 | var 21 | sdist 22 | develop-eggs 23 | .installed.cfg 24 | .pypirc 25 | 26 | # Installer logs 27 | pip-log.txt 28 | 29 | # Unit test / coverage reports 30 | .coverage 31 | .tox 32 | nosetests.xml 33 | htmlcov 34 | .cache 35 | .pytest_cache/ 36 | 37 | # Translations 38 | *.mo 39 | 40 | # Complexity 41 | output/*.html 42 | output/*/index.html 43 | 44 | # Sphinx 45 | docs/_build 46 | 47 | # PyCharm 48 | .idea 49 | .idea/* 50 | 51 | # VSCode 52 | .vscode 53 | .vscode/* 54 | 55 | # Vagrant 56 | .vagrant 57 | Vagrantfile 58 | 59 | # rope project settings 60 | .ropeproject 61 | 62 | #conda version 63 | __conda_version__.txt 64 | mbuild/version.py 65 | 66 | #virtual env 67 | .env/ 68 | 69 | # protobuf generated py file 70 | compound_pb2.py 71 | -------------------------------------------------------------------------------- /.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: 6.0.0 25 | hooks: 26 | - id: isort 27 | name: isort (python) 28 | args: [--profile=black, --line-length=80] 29 | -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- 1 | version: 2 2 | formats: 3 | - htmlzip 4 | - pdf 5 | conda: 6 | environment: docs/environment_docs.yml 7 | build: 8 | os: ubuntu-20.04 9 | tools: 10 | python: "mambaforge-4.10" 11 | sphinx: 12 | builder: html 13 | configuration: docs/conf.py 14 | fail_on_warning: False 15 | -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- 1 | # This CITATION.cff file was generated with cffinit. 2 | # Visit https://bit.ly/cffinit to generate yours today! 3 | 4 | cff-version: 1.0.0 5 | title: >- 6 | MoSDeF-GOMC: Python software for the 7 | creation of scientific workflows for the Monte 8 | Carlo simulation engine GOMC." 9 | message: "Please cite this software using these metadata and the preferred citation." 10 | type: software 11 | authors: 12 | - given-names: "Brad" 13 | family-names: Crawford 14 | affiliation: "Wayne State University" 15 | orcid: 'https://orcid.org/0000-0003-0638-7333' 16 | - given-names: Umesh 17 | family-names: Timalsina 18 | affiliation: "Vanderbilt University" 19 | orcid: 'https://orcid.org/0000-0002-5430-3993' 20 | - given-names: "Co D." 21 | family-names: Quach 22 | affiliation: "Vanderbilt University" 23 | orcid: 'https://orcid.org/0000-0002-1255-4161' 24 | - given-names: "Nicholas" 25 | family-names: Craven 26 | affiliation: "Vanderbilt University" 27 | orcid: 'https://orcid.org/0000-0002-4607-4377' 28 | - given-names: "Justin B." 29 | family-names: Gilmer 30 | affiliation: "Vanderbilt University" 31 | orcid: 'https://orcid.org/0000-0002-6915-5591' 32 | - given-names: "Clare" 33 | family-names: McCabe 34 | affiliation: "Vanderbilt University" 35 | orcid: 'https://orcid.org/0000-0002-8552-9135' 36 | - given-names: "Peter T." 37 | family-names: Cummings 38 | affiliation: "Vanderbilt University" 39 | orcid: 'https://orcid.org/0000-0002-9766-2216' 40 | - given-names: "Jeffrey" 41 | family-names: Potoff 42 | affiliation: "Wayne State University" 43 | orcid: 'https://orcid.org/0000-0002-4421-8787' 44 | 45 | repository-code: 'https://github.com/GOMC-WSU' 46 | url: 'https://github.com/GOMC-WSU' 47 | repository: 'https://github.com/GOMC-WSU/MoSDeF-GOMC' 48 | repository-artifact: 'https://github.com/GOMC-WSU/MoSDeF-GOMC/releases' 49 | abstract: >- 50 | MoSDeF-GOMC: Python software for the 51 | creation of scientific workflows for the Monte 52 | Carlo simulation engine GOMC 53 | 54 | MoSDeF-GOMC is designed to produce all the required files to run a Monte Carlo simulation, with only tens of lines of Python code. Alternately, this software's output can also build the starting files for a single residue molecules via NAMD and and the py-MCMD codes. 55 | 56 | keywords: 57 | - Python 58 | - Reproducibility 59 | - "Molecular Simulation" 60 | - "Monte Carlo" 61 | - GOMC 62 | - "computational chemistry" 63 | - chemistry 64 | - 'TRUE' 65 | - mosdef 66 | license: "MIT" 67 | preferred-citation: 68 | type: "article" 69 | authors: 70 | - given-names: "Brad" 71 | family-names: Crawford 72 | affiliation: "Wayne State University" 73 | - given-names: Umesh 74 | family-names: Timalsina 75 | affiliation: "Vanderbilt University" 76 | orcid: 'https://orcid.org/0000-0002-5430-3993' 77 | - given-names: "Co D." 78 | family-names: Quach 79 | affiliation: "Vanderbilt University" 80 | orcid: 'https://orcid.org/0000-0002-1255-4161' 81 | - given-names: "Nicholas" 82 | family-names: Craven 83 | affiliation: "Vanderbilt University" 84 | orcid: 'https://orcid.org/0000-0002-4607-4377' 85 | - given-names: "Justin B." 86 | family-names: Gilmer 87 | affiliation: "Vanderbilt University" 88 | orcid: 'https://orcid.org/0000-0002-6915-5591' 89 | - given-names: "Peter T." 90 | family-names: Cummings 91 | affiliation: "Vanderbilt University" 92 | orcid: 'https://orcid.org/0000-0002-9766-2216' 93 | - given-names: "Peter T." 94 | family-names: Cummings 95 | affiliation: "Vanderbilt University" 96 | orcid: 'https://orcid.org/0000-0002-9766-2216' 97 | - given-names: "Jeffrey" 98 | family-names: Potoff 99 | affiliation: "Wayne State University" 100 | orcid: 'https://orcid.org/0000-0002-4421-8787' 101 | title: "MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC" 102 | year: "TBD" 103 | doi: "TBD" 104 | -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | ARG PY_VERSION=3.9 2 | FROM continuumio/miniconda3:4.10.3-alpine AS builder 3 | 4 | EXPOSE 8888 5 | 6 | LABEL maintainer.name="mosdef_gomc"\ 7 | maintainer.url="https://github.com/GOMC-WSU/MoSDeF-GOMC" 8 | 9 | ENV PATH /opt/conda/bin:$PATH 10 | 11 | USER root 12 | 13 | ADD . /mosdef_gomc 14 | 15 | WORKDIR /mosdef_gomc 16 | 17 | # Create a group and user 18 | RUN addgroup -S anaconda && adduser -S anaconda -G anaconda 19 | 20 | # install the libarchive package needed by mamba 21 | RUN apk update && apk add libarchive 22 | 23 | RUN conda update conda -yq && \ 24 | conda config --set always_yes yes --set changeps1 no && \ 25 | . /opt/conda/etc/profile.d/conda.sh && \ 26 | sed -i -E "s/python.*$/python="$(PY_VERSION)"/" environment.yml && \ 27 | conda install -c conda-forge mamba && \ 28 | mamba env create --file environment.yml && \ 29 | conda activate mosdef_gomc && \ 30 | mamba install -c conda-forge nomkl jupyter python="$PY_VERSION" && \ 31 | python setup.py install && \ 32 | echo "source activate mosdef_gomc" >> \ 33 | /home/anaconda/.profile && \ 34 | conda clean -afy && \ 35 | mkdir -p /home/anaconda/data && \ 36 | chown -R anaconda:anaconda /mosdef_gomc && \ 37 | chown -R anaconda:anaconda /opt && \ 38 | chown -R anaconda:anaconda /home/anaconda 39 | 40 | 41 | WORKDIR /home/anaconda 42 | 43 | COPY devtools/docker-entrypoint.sh /entrypoint.sh 44 | 45 | RUN chmod a+x /entrypoint.sh 46 | 47 | USER anaconda 48 | 49 | ENTRYPOINT ["/entrypoint.sh"] 50 | CMD ["jupyter"] 51 | -------------------------------------------------------------------------------- /LICENSE.rst: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | With the exceptions noted below, this code is released under the MIT License: 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy of 6 | this software and associated documentation files (the "Software"), to deal in 7 | the Software without restriction, including without limitation the rights to 8 | use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of 9 | the Software, and to permit persons to whom the Software is furnished to do so, 10 | subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS 17 | FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR 18 | COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER 19 | IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN 20 | CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 21 | 22 | ---------------------------------------------------------------------- 23 | 24 | Garnett is BSD 3-Clause licensed with the following 25 | notice: 26 | 27 | BSD 3-Clause License for garnett 28 | 29 | Copyright (c) 2020 The Regents of the University of Michigan 30 | All rights reserved. 31 | 32 | Redistribution and use in source and binary forms, with or without 33 | modification, are permitted provided that the following conditions are met: 34 | 35 | 1. Redistributions of source code must retain the above copyright notice, 36 | this list of conditions and the following disclaimer. 37 | 38 | 2. Redistributions in binary form must reproduce the above copyright notice, 39 | this list of conditions and the following disclaimer in the documentation 40 | and/or other materials provided with the distribution. 41 | 42 | 3. Neither the name of the copyright holder nor the names of its contributors 43 | may be used to endorse or promote products derived from this software without 44 | specific prior written permission. 45 | 46 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 47 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 48 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 49 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR 50 | ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 51 | (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 52 | LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 53 | ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 54 | (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 55 | SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 56 | 57 | ---------------------------------------------------------------------- 58 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include LICENSE.rst 2 | global-include *.pdb *.mol2 *.smi *.xml *.xyz *.gsd *.cif *.sdf 3 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/GOMC-WSU/MoSDeF-GOMC/master.svg)](https://results.pre-commit.ci/latest/github/GOMC-WSU/MoSDeF-GOMC/master) 2 | [![CI](https://github.com/GOMC-WSU/MoSDeF-GOMC/actions/workflows/CI.yml/badge.svg)](https://github.com/GOMC-WSU/MoSDeF-GOMC/actions/workflows/CI.yml) 3 | ## MoSDeF-GOMC: 4 | 5 | ### A User-Friendly Python Interface for Creating All of the files required to run a GPU Optimized Monte Carlo (GOMC) simulation engine via the Molecular Simulation Design Framework [Molecular Simulation Design Framework (MoSDeF)](https://mosdef.org) ([MoSDeF Github](https://github.com/mosdef-hub)) software. 6 | -------- 7 | 8 | ### Overview 9 | 10 | This Python code allows the auto-generation of the [GPU Optimized Monte Carlo (GOMC)](http://gomc.eng.wayne.edu) files for a simulation, which includes the coordinate (PDB), topology (PSF), force field (FF), and the GOMC control file. This software supports various systems, force field types, and can also create the PDB, PSF, and FF files for the [NAMD](https://www.ks.uiuc.edu/Research/namd/) simulation engine. Since MoSDeF-GOMC was built from the [Molecular Simulation Design Framework (MoSDeF)](https://mosdef.org) ([MoSDeF Github](https://github.com/mosdef-hub)) platform, it provides complete integration with the MoSDeF software. 11 | 12 | ### Warning 13 | MoSDeF-GOMC is a new product continually adding functionality to provide an optimal user experience. Therefore, there could be some user-noticeable changes to this software when upgrading newer MoSDeF-GOMC versions. 14 | 15 | The original version of MoSDeF-GOMC, which uses Parmed as the software backend, will be deprecated by December 2022. This Parmed version is already replaced with the new MoSDeF-GOMC version, which uses MoSDeF's GMSO software as the new backend. We recommend that the new **GMSO** version of MoSDeF-GOMC be used because it has many new features, and the Parmed is no longer supported. 16 | 17 | ### Resources 18 | - [GOMC Github repository](https://github.com/GOMC-WSU) 19 | - [Downloading GOMC](https://github.com/GOMC-WSU/GOMC) 20 | - [Installing GOMC via GOMC manual](https://github.com/GOMC-WSU/Manual) 21 | - [MoSDeF-GOMC tutorials and examples](https://github.com/GOMC-WSU/GOMC_Examples/tree/main/MoSDef-GOMC) with [MoSDeF-GOMC YouTube videos](https://www.youtube.com/watch?v=7StVoUCGkHs&list=PLdxD0z6HRx8Y9VhwcODxAHNQBBJDRvxMf) 22 | - [GOMC YouTube channel](https://www.youtube.com/channel/UCueLGE6tuOyu-mvxIt-U1HQ/playlists) 23 | - [MoSDeF tools](https://mosdef.org/) 24 | 25 | ### Citation 26 | 27 | Please cite MoSDeF-GOMC, GOMC, and MoSDeF tools, which are provided [here](https://mosdef-gomc.readthedocs.io/en/latest/reference/citing_mosdef_gomc_python.html). 28 | 29 | ### Documentation 30 | 31 | The MoSDeF-GOMC documentation is located [here](https://mosdef-gomc.readthedocs.io/en/latest/index.html). 32 | 33 | ### Installation 34 | 35 | The recommended MoSDeF-GOMC package installation is with [mamba](https://github.com/mamba-org/mamba): 36 | 37 | `conda create --name mosdef_gomc python=3.10` 38 | 39 | `conda activate mosdef_gomc` 40 | 41 | `conda install -c conda-forge mamba` 42 | 43 | `mamba install -c conda-forge mosdef-gomc` 44 | 45 | 46 | The MoSDeF-GOMC package is also available via conda, but conda has had some issues pulling the most recent packages (user beware): 47 | 48 | `conda create --name mosdef_gomc -c conda-forge mosdef-gomc python=3.10` 49 | 50 | NOTE: conda has had some issues pulling the most recent packages, so a mamba installation is recommended. 51 | -------------------------------------------------------------------------------- /codecov.yml: -------------------------------------------------------------------------------- 1 | ignore: 2 | - "mosdef_gomc/tests" 3 | -------------------------------------------------------------------------------- /devtools/docker-entrypoint.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | . /opt/conda/etc/profile.d/conda.sh 4 | conda activate base 5 | conda activate mosdef_gomc 6 | 7 | if [ "$@" == "jupyter" ]; then 8 | jupyter notebook --no-browser --notebook-dir /home/anaconda/data --ip="0.0.0.0" 9 | else 10 | $@ 11 | fi 12 | -------------------------------------------------------------------------------- /docs/_images/mosdef_gomc_license: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | 4 | With the exceptions noted below, this code is released under the MIT License: 5 | 6 | Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: 7 | 8 | The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 9 | 10 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 11 | 12 | The method mbuild/box.py:Box._normalize_box was heavily inspired and in certain cases, copied from the garnett/trajectory.py:Trajectory._regularize_box method in the garnett python package. Garnett is BSD 3-Clause licensed with the following notice: 13 | 14 | BSD 3-Clause License for garnett 15 | 16 | Copyright (c) 2020 The Regents of the University of Michigan All rights reserved. 17 | 18 | Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 19 | 20 | Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 21 | Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 22 | Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. 23 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 24 | -------------------------------------------------------------------------------- /docs/environment_docs.yml: -------------------------------------------------------------------------------- 1 | name: mosdef_gomc_docs 2 | channels: 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - garnett 7 | - gsd=3.3.2 8 | - ipython 9 | - numpydoc 10 | - mock 11 | - sphinx_rtd_theme 12 | - nbsphinx 13 | - sphinxcontrib 14 | - pycifrw 15 | - pytest 16 | - pytest-cov 17 | - coverage 18 | - sympy 19 | - symengine 20 | - python-symengine 21 | - python>=3.10,<3.12 22 | - forcefield-utilities>=0.3.0 23 | - foyer>=0.12.1 24 | - gmso>=0.12.4 25 | - mbuild>=0.17.1 26 | - pre-commit 27 | - sphinx=6.1.1 28 | - pip 29 | - pip: 30 | - bump2version 31 | - sphinxcontrib-svg2pdfconverter 32 | - sphinxcontrib-video 33 | - sphinxcontrib-serializinghtml 34 | -------------------------------------------------------------------------------- /docs/getting_started/installation/installation.rst: -------------------------------------------------------------------------------- 1 | ============ 2 | Installation 3 | ============ 4 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 5 | :target: http://opensource.org/licenses/MIT 6 | 7 | Install with `mamba `_ (Recommended) 8 | ------------------------------------------------------------------------ 9 | :: 10 | 11 | $ conda create --name mosdef_gomc python=3.11 12 | 13 | $ conda activate mosdef_gomc 14 | 15 | $ conda install -c conda-forge mamba 16 | 17 | $ mamba install -c conda-forge mosdef-gomc python=3.11 18 | 19 | 20 | Install with `conda `_ 21 | ------------------------------------------------------------ 22 | :: 23 | 24 | $ conda install -c conda-forge mosdef-gomc 25 | 26 | 27 | NOTE: conda has had some issues pulling the most recent packages, so a mamba installation is recommended. 28 | 29 | Install an editable version from the source code 30 | ------------------------------------------------ 31 | 32 | It is good practice to use a pre-packaged Python distribution like 33 | `Miniconda `_, 34 | which ensures all of the dependencies are installed:: 35 | 36 | $ git clone https://github.com/GOMC-WSU/MoSDeF-GOMC 37 | $ cd mosdef_gomc 38 | $ conda env create -f environment.yml 39 | $ conda activate mosdef_gomc 40 | $ pip install -e . 41 | 42 | .. note:: 43 | The above installation instructions are for OSX and Unix. If you are using Windows, please use a virtual machine or the Linux subsystem, as some components of this software and its dependencies may not be fully compatible with Windows. 44 | 45 | 46 | Install pre-commit 47 | ------------------ 48 | 49 | The `pre-commit `_ packages are utilized to maintain uniform code formatting, which is auto-installed in the mosdef_gomc environment. 50 | 51 | To check all the file, you can run:: 52 | 53 | $ pre-commit run --all-files 54 | 55 | 56 | Supported Python Versions 57 | ------------------------- 58 | 59 | Python 3.10 and 3.11 are officially supported and tested during development and with the final product. 60 | Python versions older than 3.10 may work, but there is no guarantee. 61 | 62 | Testing your installation 63 | ------------------------- 64 | 65 | MoSDeF-GOMC uses `pytest `_ to test the code for accuracy, possible errors, code changes, or if the existing implementation is correct. 66 | The pytest package is auto-installed in the ``mosdef_gomc`` environment. 67 | 68 | To run these unit tests, run the following from the base directory:: 69 | 70 | $ pytest -v 71 | 72 | Building the documentation 73 | -------------------------- 74 | 75 | ``MoSDeF-GOMC`` documentation is all built using `sphinx `_. 76 | The ``sphinx`` software may need to be installed separately to avoid dependency conflicts. 77 | If ``sphinx`` is not automatically provided, the correct ``sphinx`` package can be build after creating 78 | a new conda environment using the ``environment_docs.yml`` file in the ``MoSDeF-GOMC/docs`` 79 | directory, located on ``MoSDeF-GOMC`` GitHub's main repository or GitHub's releases for a specific version. 80 | 81 | The ``docs`` can be built locally with the following commands when in the ``docs`` directory:: 82 | 83 | $ make html 84 | -------------------------------------------------------------------------------- /docs/getting_started/quick_start/build_a_system_and_write_all_files.rst: -------------------------------------------------------------------------------- 1 | Build A System and Write All Files 2 | ================================== 3 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 4 | :target: http://opensource.org/licenses/MIT 5 | 6 | 7 | All-Atom (AA) Hexane and Pentane System 8 | --------------------------------------- 9 | 10 | .. note:: 11 | NAMD can directly use these files, but the NAMD control file is not written with this software and needs to be provided by the user. 12 | 13 | Import the required mbuild package. 14 | 15 | .. code:: ipython3 16 | 17 | import mbuild as mb 18 | import unyt as u 19 | import mosdef_gomc.formats.gmso_charmm_writer as mf_charmm 20 | import mosdef_gomc.formats.gmso_gomc_conf_writer as gomc_control 21 | 22 | 23 | Construct a hexane and pentane all-atom (AA) system using the OPLS-AA force field (FF), 24 | which is a standard FF supplied with `foyer `_. 25 | The molecules are built via `smiles strings `_. 26 | The hexane and pentane residues are named `"HEX"` and `"PEN"`, respectively. 27 | All the `GPU Optimized Monte Carlo (GOMC) `_ files for conducting a are written, including the **GOMC** control file. The GOMC control file selects many defaults, minimizes novice user errors, and allows expert users to change GOMC parameters. 28 | 29 | .. code:: ipython3 30 | 31 | # GOMC Example for hexane and pentane the NPT Ensemble via MoSDeF. 32 | 33 | # Specify the box dimensions, number of molecules, and mol ratios. 34 | import mbuild as mb 35 | import unyt as u 36 | import mosdef_gomc.formats.gmso_charmm_writer as mf_charmm 37 | import mosdef_gomc.formats.gmso_gomc_conf_writer as gomc_control 38 | 39 | # Create the hexane and pentane molecules with residue names. 40 | hexane =mb.load('CCCCCC', smiles=True) 41 | hexane.name = 'HEX' 42 | 43 | pentane = mb.load('CCCCC', smiles=True) 44 | pentane.name = 'PEN' 45 | 46 | # Build the main liquid simulation box. 47 | # NOTE: mBuild dimensions are in nm, and density in kg/m^3. 48 | box_liq = mb.fill_box(compound=[hexane, pentane], 49 | compound_ratio=[0.5, 0.5], 50 | density=700, 51 | box=[4.5, 4.5, 4.5] 52 | ) 53 | 54 | # Build the Charmm object, which is required to write the 55 | # FF (.inp), psf, pdb, and GOMC control files. 56 | charmm = mf_charmm.Charmm(box_liq, 57 | 'NPT_hexane_pentane', 58 | structure_box_1=None, 59 | filename_box_1=None, 60 | ff_filename="NPT_hexane_pentane_FF" , 61 | forcefield_selection={ 62 | hexane.name: 'oplsaa' , 63 | pentane.name: 'oplsaa' 64 | }, 65 | residues=[hexane.name, pentane.name], 66 | ) 67 | 68 | ## Write the write the FF (.inp), psf, pdb, and GOMC control files 69 | charmm.write_inp() 70 | charmm.write_psf() 71 | charmm.write_pdb() 72 | 73 | gomc_control.write_gomc_control_file(charmm, 74 | 'in_NPT.conf', 75 | 'NPT', 76 | 100, 77 | 300 * u.K, 78 | input_variables_dict={"Pressure": 10 * u.bar} 79 | ) 80 | -------------------------------------------------------------------------------- /docs/getting_started/quick_start/gomc_examples_repository.rst: -------------------------------------------------------------------------------- 1 | Examples Repositories 2 | ===================== 3 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 4 | :target: http://opensource.org/licenses/MIT 5 | 6 | Simple Examples 7 | --------------- 8 | 9 | .. note:: 10 | NAMD can directly use these files, but the NAMD control file is not written with this software and needs to be provided by the user. 11 | 12 | `Simple MoSDeF-GOMC examples `_ are located on the **GOMC** Github page 13 | 14 | 15 | Full Examples (Entire Signac Workflows) 16 | --------------------------------------- 17 | 18 | `Complex MoSDeF-GOMC examples `_ are located on the **GOMC** Github page. These complete examples use `Signac `_ to build the systems, manage their status, submit them to the computer resources, and perform the data analysis 19 | -------------------------------------------------------------------------------- /docs/getting_started/quick_start/quick_start.rst: -------------------------------------------------------------------------------- 1 | .. _QuickStart: 2 | 3 | ----------- 4 | Quick Start 5 | ----------- 6 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 7 | :target: http://opensource.org/licenses/MIT 8 | 9 | 10 | .. note:: 11 | **MoSDeF-GOMC** uses the **MoSDeF** packages to build the chemical system, then **MoSDeF-GOMC** generates all the required files to conduct a GOMC simulation. **NAMD** can also use the **MoSDeF-GOMC** software to generate the system (PDB and PSF files) and force field files, provided they are single residue molecules and the user produces their own **NAMD** control file. 12 | 13 | 14 | The following examples are provided as a python file, as well as interactive `jupyter `_ notebooks for the simple examples. 15 | 16 | 17 | .. toctree:: 18 | 19 | build_a_system_and_write_all_files 20 | gomc_examples_repository 21 | -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- 1 | MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC 2 | ================================================================================================================ 3 | 4 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 5 | :target: http://opensource.org/licenses/MIT 6 | 7 | 8 | The `GPU Optimized Monte Carlo (GOMC) `_ simulation engine is one of the fastest open-source Monte Carlo engines. `Molecular Simulation Design Framework (MoSDeF) `_ software is an open-source software package that efficiently constructs simple or complex chemical systems, applies the force field parameters, and writes several simulation input files. 9 | **MoSDeF-GOMC** uses the power of **MoSDeF** to build the traditional chemical engineering system, while **MoSDeF-GOMC** 10 | generates all the required files to perform a **GOMC** simulation. 11 | 12 | The **MoSDeF-GOMC** software is compatible with the following software or simulation methods, when the files are generated with the Lennard-Jones (LJ) non-bonded potential: 13 | #. The `NAMD `_ molecular dynamics software: The NAMD control file needs to be created by another means, but all the other files (PDB, PSF, and force field files) are compatible. 14 | 15 | #. The `py-MCMD `_ software (Hybrid Monte Carlo and molecular dynamics simulations via **GOMC** and **NAMD**): All files are compatible except the GOMC control file (PDB, PSF, and force field files) are compatible. 16 | 17 | #. Switching back and forth, in any order or duration, between a **GOMC** and **NAMD** simulations, allowing faster equilibrium for **GOMC** simulations and many other advantages. The newest **GOMC** versions also retain the atom/bead velocities and pass them back to **NAMD**. 18 | 19 | 20 | **MoSDeF-GOMC Highlights**: 21 | #. With tens of lines of **MoSDeF-GOMC** code, you can generate all the required files to conduct a **GOMC** simulation (see `Simple MoSDeF-GOMC examples `_). 22 | 23 | #. **MoSDeF-GOMC** is designed to automate the simulation workflow, allowing high-throughput workflows with **GOMC** or **NAMD**, where `signac `_ can be utilized to manage the simulations, data storage, and analysis. 24 | 25 | #. **MoSDeF-GOMC** lowers the barrier of entry for novice users. 26 | 27 | #. **MoSDeF-GOMC** and **MoSDeF** permit reproducible simulations, as these automated simulation workflows can build, simulate, and analyze the data in a repeatable manner. This allows the simulation workflows to be easily transferred, replicated, or expanded upon within or outside existing teams. 28 | 29 | 30 | 31 | .. toctree:: 32 | :caption: Overview 33 | :maxdepth: 2 34 | 35 | overview/general_info 36 | overview/supported_chemical_systems 37 | 38 | .. toctree:: 39 | :caption: Getting Started 40 | :maxdepth: 2 41 | 42 | getting_started/installation/installation 43 | getting_started/quick_start/quick_start 44 | 45 | .. toctree:: 46 | :caption: Topic Guides 47 | :maxdepth: 2 48 | 49 | topic_guides/data_structures 50 | topic_guides/load_data 51 | 52 | .. toctree:: 53 | :caption: Reference 54 | :maxdepth: 2 55 | 56 | reference/units 57 | reference/user_notices 58 | reference/credits 59 | reference/citing_mosdef_gomc_python 60 | -------------------------------------------------------------------------------- /docs/overview/general_info.rst: -------------------------------------------------------------------------------- 1 | 2 | General Information 3 | =================== 4 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 5 | :target: http://opensource.org/licenses/MIT 6 | 7 | 8 | MoSDeF-GOMC Basics 9 | ------------------ 10 | The `Molecular Simulation Design Framework (MoSDeF) `_ 11 | software is the base software for **MoSDeF-GOMC**, which builds and force fields the systems inside the **MoSDeF-GOMC**. 12 | This **MoSDeF-GOMC** software generates the required files for simulating a system using 13 | the `GPU Optimized Monte Carlo (GOMC) `_ or the 14 | `NAMD `_ molecular dynamics software. The **MoSDeF-GOMC** software 15 | builds all the required files (PDB, PSF, force field, and **GOMC** control files) to conduct a **GOMC** simulation. 16 | 17 | The **MoSDeF-GOMC** software is compatible with the following software or simulation methods, when the files are generated with the Lennard-Jones (LJ) non-bonded potential: 18 | #. The `NAMD `_ molecular dynamics software: The NAMD control file needs to be created by another means, but all the other files (PDB, PSF, and force field files) are compatible. 19 | 20 | #. The `py-MCMD `_ software (Hybrid Monte Carlo and molecular dynamics simulations via **GOMC** and **NAMD**): All files are compatible except the GOMC control file (PDB, PSF, and force field files) are compatible. 21 | 22 | #. Switching back and forth, in any order or duration, between a **GOMC** and **NAMD** simulations, allowing faster equilibrium for **GOMC** simulations and many other advantages. The newest **GOMC** versions also retain the atom/bead velocities and pass them back to **NAMD**. 23 | 24 | 25 | The **MoSDeF-GOMC** software creates all these files using only tens of lines of Python code. 26 | The **MoSDeF-GOMC** and **MoSDeF** tools permit simulation reproducibility across a variety of simulation engines, 27 | removing the requirement of expert knowledge in all the engines to repeat, continue, or advance the existing research. 28 | Additionally, the **MoSDeF-GOMC** and **MoSDeF** software permits the auto-generation of numerous and distinct 29 | systems, allowing large-scale screening of materials and chemicals via `signac `_ to manage 30 | the simulations and data. 31 | 32 | .. note:: 33 | The using **MoSDeF-GOMC** software to setup the **GOMC** and **NAMD** simulations, 34 | is made even easier via the 35 | `MoSDeF-GOMC Examples `_ and the 36 | `GOMC Documentation `_, which contains links to the GOMC Manual, with 37 | `GOMC YouTube tutorial videos `_. 38 | For the Lennard-Jones (LJ) non-bonded interactions, the MoSDeF-GOMC's PDB, PSF, and force field files are 39 | identical to the NAMD files for the traditional chemical engineering simulations, unless there are fixed bonds 40 | and angles in the GOMC force field files. Changing the fixed bonds and angles between the GOMC and NAMD 41 | force field files is as simple as changing one (1) variable and rerunning that line of code, 42 | making a separate GOMC and NAMD files for the same system. Making separate files may be needed when 43 | running a hybrid Monte Carlo and molecular dynamics (GOMC and NAMD) simulation with the 44 | `py-MCMD `_ software . 45 | 46 | MoSDeF-GOMC is a part of the MoSDeF ecosystem 47 | --------------------------------------------- 48 | The **MoSDeF-GOMC** software is a liaison between the 49 | `Molecular Simulation Design Framework (MoSDeF) `_ software suite and the 50 | **GOMC** simulation engine. 51 | The MoSDeF libraries also supports various simulation engines, 52 | including `Cassandra `_, 53 | `GOMC `_, 54 | `GROMACS `_, 55 | `HOOMD-blue `_, and 56 | `LAMMPS `_. 57 | The **MoSDeF-GOMC** and **MoSDeF** libraries permit reproducibility simulations 58 | across a wide range of simulation engines, eliminating the need to be an expert in every simulation engine 59 | to replicate or expand upon the existing research. These software packages can auto-produce a variety of different chemical systems, 60 | permitting large-scale screening of chemicals and materials using `signac `_ to manage the simulations, data, and analysis. 61 | 62 | The **MoSDeF** software is comprised the following core packages: 63 | * `mBuild `_ -- A hierarchical, component based molecule builder 64 | 65 | * `foyer `_ -- A package for atom-typing as well as applying and disseminating forcefields 66 | 67 | * `GMSO `_ -- Flexible storage of chemical topology for molecular simulation 68 | -------------------------------------------------------------------------------- /docs/overview/supported_chemical_systems.rst: -------------------------------------------------------------------------------- 1 | 2 | Supported Chemical Systems 3 | ========================== 4 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 5 | :target: http://opensource.org/licenses/MIT 6 | 7 | Traditional Chemical Engineering Systems 8 | ---------------------------------------- 9 | 10 | The `MoSDeF-GOMC software `_ is currently capable of 11 | generating traditional chemical engineering systems that are not proteins or other molecules 12 | requiring multiple residue names per molecule, covering various systems. 13 | **MoSDeF-GOMC** only supports molecules with a single residue name and will support a protein if it has only one (1) residue name per molecule. 14 | In the future, we plan to support these molecules, which require multiple residue names per molecule. 15 | 16 | 17 | 18 | Non-Traditional Chemical Engineering Systems 19 | -------------------------------------------- 20 | 21 | Non-traditional chemical engineering systems are proteins or other molecules requiring multiple residue names per molecule. Currently, the **MoSDeF-GOMC** 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. 22 | -------------------------------------------------------------------------------- /docs/reference/citing_mosdef_gomc_python.rst: -------------------------------------------------------------------------------- 1 | ====== 2 | Citing 3 | ====== 4 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 5 | :target: http://opensource.org/licenses/MIT 6 | 7 | If you use this code for your research, please cite for following sources: 8 | 9 | 10 | `The Journal website `_: 11 | 12 | **ACS** 13 | 14 | Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey. MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC. J. Chem. Inf. Model. 2023, 63(4), 1218-1228. 15 | 16 | **BibTeX** 17 | 18 | .. code-block:: bibtex 19 | 20 | @article{MOSDEF_GOMC_2023_paper, 21 | author = {Crawford, Brad and Timalsina, Umesh and Quach, Co D. and Craven, Nicholas C. and Gilmer, Justin B. and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey J.}, 22 | title = {MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC}, 23 | journal = {Journal of Chemical Information and Modeling}, 24 | volume = {63}, 25 | number = {4}, 26 | pages = {1218-1228}, 27 | year = {2023}, 28 | doi = {10.1021/acs.jcim.2c01498}, 29 | note ={PMID: 36791286}, 30 | 31 | url = { 32 | https://doi.org/10.1021/acs.jcim.2c01498 33 | 34 | }, 35 | } 36 | 37 | Download as :download:`BibTeX ` or :download:`RIS ` 38 | 39 | 40 | `The GitHub repository `_: 41 | 42 | **ACS** 43 | 44 | Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey. MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC, https://github.com/GOMC-WSU/MoSDeF-GOMC, 2022. 45 | 46 | **BibTeX** 47 | 48 | .. code-block:: bibtex 49 | 50 | @Inbook{MOSDEF_GOMC_2022_python, 51 | author = "Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey", 52 | title = "MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC", 53 | year = "2022", 54 | publisher = "Github", 55 | url = "https://github.com/GOMC-WSU/MoSDeF-GOMC" 56 | } 57 | 58 | Download as :download:`BibTeX ` or :download:`RIS ` 59 | 60 | 61 | `The Zenodo repository `_: 62 | 63 | **ACS** 64 | 65 | Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey. MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC, https://doi.org/10.5281/zenodo.7217632, 2022. 66 | 67 | **BibTeX** 68 | 69 | .. code-block:: bibtex 70 | 71 | @software{MOSDEF_GOMC_2022_zenodo, 72 | author = "Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey", 73 | title = "MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC", 74 | year = "2022", 75 | publisher = "Zenodo", 76 | url = "https://doi.org/10.5281/zenodo.5142483", 77 | doi = "10.5281/zenodo.721763" 78 | } 79 | 80 | Download as :download:`BibTeX ` or :download:`RIS ` 81 | 82 | 83 | 84 | Please also cite the **MoSDeF** software: 85 | * `mBuild `_ -- A hierarchical, component based molecule builder 86 | 87 | * `foyer `_ -- A package for atom-typing as well as applying and disseminating forcefields 88 | 89 | * `GMSO `_ -- Flexible storage of chemical topology for molecular simulation 90 | -------------------------------------------------------------------------------- /docs/reference/credits.rst: -------------------------------------------------------------------------------- 1 | ======= 2 | Credits 3 | ======= 4 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 5 | :target: http://opensource.org/licenses/MIT 6 | 7 | MoSDeF-GOMC developers: 8 | 9 | **Brad Crawford** - Creator, developer, and maintainer 10 | 11 | **Umesh Timalsina** - Developer 12 | 13 | **Co Quach** - Developer 14 | 15 | **Nicholas Craven** - Developer 16 | 17 | **Justin Gilmer** - Developer 18 | 19 | **Clare McCabe** - Advisor 20 | 21 | **Peter T. Cummings** - Advisor 22 | 23 | **Jeffrey Potoff** - Advisor and maintainer 24 | 25 | 26 | `MoSDeF-GOMC `_ was created and developed with a collaborative effort between **Wayne State University** and **Vanderbilt University**, which included the `GPU Optimized Monte Carlo (GOMC) `_ and `Molecular Simulation Design Framework (MoSDeF) `_ teams. 27 | 28 | The **MoSDeF-GOMC** software was supported via National Science Foundation (**NSF**) grants OAC-1835713, OAC-1835874, and CBET-2052438. Any statements stated or expressed are solely those of the **MoSDeF-GOMC** software or developers and not the **NSF**. 29 | -------------------------------------------------------------------------------- /docs/reference/mosdef_gomc_paper.bib: -------------------------------------------------------------------------------- 1 | @article{MOSDEF_GOMC_2023_paper, 2 | author = {Crawford, Brad and Timalsina, Umesh and Quach, Co D. and Craven, Nicholas C. and Gilmer, Justin B. and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey J.}, 3 | title = {MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC}, 4 | journal = {Journal of Chemical Information and Modeling}, 5 | volume = {63}, 6 | number = {4}, 7 | pages = {1218-1228}, 8 | year = {2023}, 9 | doi = {10.1021/acs.jcim.2c01498}, 10 | note ={PMID: 36791286}, 11 | 12 | URL = { 13 | https://doi.org/10.1021/acs.jcim.2c01498 14 | 15 | }, 16 | eprint = { 17 | https://doi.org/10.1021/acs.jcim.2c01498 18 | 19 | } 20 | 21 | } 22 | -------------------------------------------------------------------------------- /docs/reference/mosdef_gomc_paper.ris: -------------------------------------------------------------------------------- 1 | TY - JOUR 2 | T1 - MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC 3 | AU - Crawford, Brad 4 | AU - Timalsina, Umesh 5 | AU - Quach, Co D. 6 | AU - Craven, Nicholas C. 7 | AU - Gilmer, Justin B. 8 | AU - McCabe, Clare 9 | AU - Cummings, Peter T. 10 | AU - Potoff, Jeffrey J. 11 | Y1 - 2023/02/27 12 | PY - 2023 13 | DA - 2023/02/27 14 | N1 - doi: 10.1021/acs.jcim.2c01498 15 | DO - 10.1021/acs.jcim.2c01498 16 | T2 - Journal of Chemical Information and Modeling 17 | JF - Journal of Chemical Information and Modeling 18 | JO - J. Chem. Inf. Model. 19 | SP - 1218 20 | EP - 1228 21 | VL - 63 22 | IS - 4 23 | PB - American Chemical Society 24 | SN - 1549-9596 25 | M3 - doi: 10.1021/acs.jcim.2c01498 26 | UR - https://doi.org/10.1021/acs.jcim.2c01498 27 | ER - 28 | -------------------------------------------------------------------------------- /docs/reference/mosdef_gomc_python.bib: -------------------------------------------------------------------------------- 1 | @Inbook{MOSDEF_GOMC_2022_github, 2 | author = "Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey", 3 | title = "MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC", 4 | year = "2022", 5 | publisher = "Github", 6 | url = "https://github.com/GOMC-WSU/MoSDeF-GOMC" 7 | } 8 | -------------------------------------------------------------------------------- /docs/reference/mosdef_gomc_python.ris: -------------------------------------------------------------------------------- 1 | TY - 2 | AU - Crawford, Brad 3 | AU - Timalsina, Umesh 4 | AU - Quach, Co 5 | AU - Craven, Nicholas 6 | AU - Gilmer, Justin 7 | AU - McCabe, Clare 8 | AU - Cummings, Peter T. 9 | AU - Potoff, Jeffrey 10 | ED - 11 | ED - 12 | ED - 13 | PY - 2022 14 | DA - 2022 15 | TI - MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC 16 | BT - 17 | SP - 18 | EP - 19 | PB - 20 | CY - 21 | AB - 22 | SN - 23 | UR - https://github.com/GOMC-WSU/MoSDeF-GOMC 24 | DO - 25 | ID - mosdef_gomc_python_2022 26 | ER - 27 | -------------------------------------------------------------------------------- /docs/reference/mosdef_gomc_zenodo.bib: -------------------------------------------------------------------------------- 1 | @software{MOSDEF_GOMC_2022_zenodo, 2 | author = {Crawford, Brad and 3 | Timalsina, Umesh and 4 | Quach, Co D. and 5 | Craven, Nicholas and 6 | Gilmer, Justin B. and 7 | McCabe, Clare and 8 | Cummings, Peter T. and 9 | Potoff, Jeffrey}, 10 | title = {{MoSDeF-GOMC: Python software for the creation of 11 | scientific workflows for the Monte Carlo 12 | simulation engine GOMC}}, 13 | month = oct, 14 | year = 2022, 15 | publisher = {Zenodo}, 16 | version = {1.0.0}, 17 | doi = {10.5281/zenodo.7217632}, 18 | url = {https://doi.org/10.5281/zenodo.7217632} 19 | } 20 | -------------------------------------------------------------------------------- /docs/reference/mosdef_gomc_zenodo.ris: -------------------------------------------------------------------------------- 1 | TY - 2 | AU - Crawford, Brad 3 | AU - Timalsina, Umesh 4 | AU - Quach, Co 5 | AU - Craven, Nicholas 6 | AU - Gilmer, Justin 7 | AU - McCabe, Clare 8 | AU - Cummings, Peter T. 9 | AU - Potoff, Jeffrey 10 | ED - 11 | ED - 12 | ED - 13 | PY - 2022 14 | DA - 2022 15 | TI - MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC 16 | BT - 17 | SP - 18 | EP - 19 | PB - 20 | CY - 21 | AB - 22 | SN - 23 | UR - https://doi.org/10.5281/zenodo.7217632 24 | DO - 10.5281/zenodo.721763 25 | ID - MOSDEF_GOMC_2022_zenodo 26 | ER - 27 | -------------------------------------------------------------------------------- /docs/reference/units.rst: -------------------------------------------------------------------------------- 1 | ===== 2 | Units 3 | ===== 4 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 5 | :target: http://opensource.org/licenses/MIT 6 | 7 | **MoSDeF-GOMC** uses the `unyt `_ package for all its unit systems, except if they are unitless values. 8 | 9 | .. note:: 10 | The **MoSDeF-GOMC** uses the `Molecular Simulation Design Framework (MoSDeF) `_ software. Therefore, for all the compatible unit systems, please see the following packages: 11 | 12 | * `mBuild `_ -- A hierarchical, component based molecule builder 13 | 14 | * `foyer `_ -- A package for atom-typing as well as applying and disseminating forcefields 15 | 16 | * `GMSO `_ -- Flexible storage of chemical topology for molecular simulation 17 | 18 | 19 | .. note:: 20 | The **GOMC** and **NAMD** file units can be found in the :ref:`DataStructures` section for the PDB, PSF, and force field files, and the `GOMC input `_ and `GOMC output `_ (**GOMC** control file writer). **NAMD's** file units are the same as **GOMC's** when using the non-bonded Lennard-Jones (LJ) interactions. 21 | -------------------------------------------------------------------------------- /docs/reference/user_notices.rst: -------------------------------------------------------------------------------- 1 | ============ 2 | User Notices 3 | ============ 4 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 5 | :target: http://opensource.org/licenses/MIT 6 | 7 | .. warning:: 8 | The original version of **MoSDeF-GOMC**, which uses **Parmed** as the software backend, will be deprecated by December 2022. This **Parmed** version is already replaced with the new **MoSDeF-GOMC** version, which uses **MoSDeF's GMSO** software as the new backend. We recommend that the new **GMSO** version of **MoSDeF-GOMC** be used because it has many new features, and the **Parmed** is no longer supported. 9 | 10 | The new **MoSDeF-GOMC** version using GMSO allows for a more flexible and better user experience as it has the following new features: 11 | 12 | #. The ability to use Lennard-Jones (LJ) and the Mie potential individually or in combination for non-bonded interactions. The Exp6 (Buckingham) non-bonded potential will be added in the future. 13 | 14 | #. The user can build a force field file using the **GMSO** formatted XML, which allows the user to enter the equations and units for the non-bonded and bonded interactions. This includes different dihedral forms (RB-torsions, OPLS, and periodic dihedrals) and the ability to use the Kelvin energy units. Provided the equation form is permitted in the **MoSDeF-GOMC** software, **MoSDeF-GOMC** automatically converts them to the usable form and scales the coefficients accordingly 15 | 16 | #. All **MoSDeF-GOMC** functions now require the `unyt `_ package units unless the values are unitless, ensuring the user enters the proper units. **MoSDeF-GOMC** will internally handle the unit conversions and write the files with the correct units. 17 | 18 | #. Automatic application of the mixing/combining rules, if provided in the force field XML files. 19 | 20 | #. Other new features exist, so please see the **MoSDeF-GOMC** documentation for more features. 21 | -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- 1 | unyt 2 | gsd 3 | sphinx 4 | ele 5 | nbsphinx 6 | lark-parser 7 | requests 8 | mock 9 | numpydoc 10 | anaconda 11 | widgetsnbextension 12 | ipywidgets 13 | sphinxcontrib 14 | sphinx_rtd_theme 15 | sphinxcontrib-svg2pdfconverter 16 | sphinxcontrib-video 17 | ipykernel 18 | -------------------------------------------------------------------------------- /docs/topic_guides/data_structures.rst: -------------------------------------------------------------------------------- 1 | .. _DataStructures: 2 | 3 | =============== 4 | Data Structures 5 | =============== 6 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 7 | :target: http://opensource.org/licenses/MIT 8 | 9 | 10 | CHARMM-style PDB, PSF, and Force Field File Writers 11 | --------------------------------------------------- 12 | 13 | .. autoclass:: mosdef_gomc.formats.gmso_charmm_writer.Charmm 14 | :special-members: __init__ 15 | :members: 16 | 17 | 18 | GOMC Control File Writer 19 | ------------------------ 20 | 21 | .. automodule:: mosdef_gomc.formats.gmso_gomc_conf_writer 22 | :members: write_gomc_control_file, print_required_input 23 | 24 | 25 | 26 | 27 | 28 | NAMD Control File Writer 29 | ------------------------ 30 | 31 | The NAMD control file writer is not currently available. 32 | 33 | 34 | 35 | MoSDeF software functions 36 | ------------------------- 37 | 38 | The **MosDeF-GOMC** was built on the **MosDeF** ecosystem. Therefore, please see the **MoSDeF** software documentation for details on the respective packages: 39 | * `mBuild `_ -- A hierarchical, component based molecule builder 40 | 41 | * `foyer `_ -- A package for atom-typing as well as applying and disseminating forcefields 42 | 43 | * `GMSO `_ -- Flexible storage of chemical topology for molecular simulation 44 | -------------------------------------------------------------------------------- /docs/topic_guides/load_data.rst: -------------------------------------------------------------------------------- 1 | ============ 2 | Loading Data 3 | ============ 4 | .. image:: https://img.shields.io/badge/license-MIT-blue.svg 5 | :target: http://opensource.org/licenses/MIT 6 | 7 | 8 | Please see the :ref:`QuickStart` section for how to load the files and the general format of the loaded files. 9 | 10 | The **MosDeF-GOMC** was built on the **MosDeF** ecosystem. Therefore, please see the **MoSDeF** software documentation for details on the respective packages: 11 | * `mBuild `_ -- A hierarchical, component based molecule builder 12 | 13 | * `foyer `_ -- A package for atom-typing as well as applying and disseminating forcefields 14 | 15 | * `GMSO `_ -- Flexible storage of chemical topology for molecular simulation 16 | -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- 1 | name: mosdef_gomc 2 | channels: 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - garnett 7 | - gsd=3.3.2 8 | - ipython 9 | - numpydoc 10 | - mock 11 | - sphinx_rtd_theme 12 | - nbsphinx 13 | - sphinxcontrib 14 | - pycifrw 15 | - pytest 16 | - pytest-cov 17 | - coverage 18 | - sympy 19 | - symengine 20 | - python-symengine 21 | - python>=3.10,<3.12 22 | - forcefield-utilities>=0.3.0 23 | - foyer>=0.12.1 24 | - gmso>=0.12.4 25 | - mbuild>=0.17.1 26 | - pre-commit 27 | - sphinx=6.1.1 28 | - pip 29 | - pip: 30 | - bump2version 31 | - sphinxcontrib-svg2pdfconverter 32 | - sphinxcontrib-video 33 | - sphinxcontrib-serializinghtml 34 | -------------------------------------------------------------------------------- /mosdef_gomc/__init__.py: -------------------------------------------------------------------------------- 1 | """MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC""" 2 | 3 | from mosdef_gomc.formats.gmso_charmm_writer import Charmm 4 | from mosdef_gomc.formats.gmso_gomc_conf_writer import GOMCControl 5 | 6 | __version__ = "1.4.0" 7 | -------------------------------------------------------------------------------- /mosdef_gomc/formats/__init__.py: -------------------------------------------------------------------------------- 1 | """Format library for MoSDeF-GOMC, for the GOMC Engine""" 2 | -------------------------------------------------------------------------------- /mosdef_gomc/formats/charmm_writer.py: -------------------------------------------------------------------------------- 1 | class Charmm: 2 | def __init__( 3 | self, 4 | structure_box_0, 5 | filename_box_0, 6 | structure_box_1=None, 7 | filename_box_1=None, 8 | non_bonded_type="LJ", 9 | forcefield_selection=None, 10 | residues=None, 11 | detect_forcefield_style=True, 12 | gomc_fix_bonds_angles=None, 13 | gomc_fix_bonds=None, 14 | gomc_fix_angles=None, 15 | bead_to_atom_name_dict=None, 16 | fix_residue=None, 17 | fix_residue_in_box=None, 18 | set_residue_pdb_occupancy_to_1=None, 19 | ff_filename=None, 20 | reorder_res_in_pdb_psf=False, 21 | ): 22 | # depreciation error that charmm_writer has been depreciated 23 | depreciation_error = ( 24 | "The mosdef_gomc 'charmm_writer.py' has been depreciated, and the entire 'charmm_writer.py' " 25 | "file will be removed/deleted soon." 26 | "The this only effects the mosdef-gomc 'charmm_writer' parmed version. The GMSO version, " 27 | "'gmso_charmm_writer.py', has replaced it with more features, so please use this GMSO version." 28 | ) 29 | raise ModuleNotFoundError(depreciation_error) 30 | -------------------------------------------------------------------------------- /mosdef_gomc/formats/gomc_conf_writer.py: -------------------------------------------------------------------------------- 1 | class GOMCControl: 2 | def __init__( 3 | self, 4 | charmm_object, 5 | ensemble_type, 6 | RunSteps, 7 | Temperature, 8 | ff_psf_pdb_file_directory=None, 9 | check_input_files_exist=True, 10 | Restart=False, 11 | RestartCheckpoint=False, 12 | ExpertMode=False, 13 | Parameters=None, 14 | Coordinates_box_0=None, 15 | Structure_box_0=None, 16 | Coordinates_box_1=None, 17 | Structure_box_1=None, 18 | binCoordinates_box_0=None, 19 | extendedSystem_box_0=None, 20 | binVelocities_box_0=None, 21 | binCoordinates_box_1=None, 22 | extendedSystem_box_1=None, 23 | binVelocities_box_1=None, 24 | input_variables_dict=None, 25 | ): 26 | depreciation_error = ( 27 | "The mosdef_gomc 'gomc_conf_writer.py' has been depreciated, and the entire 'gomc_conf_writer.py' " 28 | "file will be removed/deleted soon." 29 | "The this only effects the mosdef-gomc 'gomc_conf_writer' parmed version. The GMSO version, " 30 | "'gmso_gomc_conf_writer.py', has replaced it with more features, so please use this GMSO version." 31 | ) 32 | raise ModuleNotFoundError(depreciation_error) 33 | 34 | 35 | # user callable function to write the GOMC control file 36 | def write_gomc_control_file( 37 | charmm_object, 38 | conf_filename, 39 | ensemble_type, 40 | RunSteps, 41 | Temperature, 42 | ff_psf_pdb_file_directory=None, 43 | check_input_files_exist=True, 44 | Restart=False, 45 | RestartCheckpoint=False, 46 | ExpertMode=False, 47 | Parameters=None, 48 | Coordinates_box_0=None, 49 | Structure_box_0=None, 50 | Coordinates_box_1=None, 51 | Structure_box_1=None, 52 | binCoordinates_box_0=None, 53 | extendedSystem_box_0=None, 54 | binVelocities_box_0=None, 55 | binCoordinates_box_1=None, 56 | extendedSystem_box_1=None, 57 | binVelocities_box_1=None, 58 | input_variables_dict=None, 59 | ): 60 | GOMCControl( 61 | charmm_object, 62 | ensemble_type, 63 | RunSteps, 64 | Temperature, 65 | ff_psf_pdb_file_directory=ff_psf_pdb_file_directory, 66 | check_input_files_exist=check_input_files_exist, 67 | Restart=Restart, 68 | RestartCheckpoint=RestartCheckpoint, 69 | ExpertMode=ExpertMode, 70 | Parameters=Parameters, 71 | Coordinates_box_0=Coordinates_box_0, 72 | Structure_box_0=Structure_box_0, 73 | Coordinates_box_1=Coordinates_box_1, 74 | Structure_box_1=Structure_box_1, 75 | binCoordinates_box_0=binCoordinates_box_0, 76 | extendedSystem_box_0=extendedSystem_box_0, 77 | binVelocities_box_0=binVelocities_box_0, 78 | binCoordinates_box_1=binCoordinates_box_1, 79 | extendedSystem_box_1=extendedSystem_box_1, 80 | binVelocities_box_1=binVelocities_box_1, 81 | input_variables_dict=input_variables_dict, 82 | ) 83 | -------------------------------------------------------------------------------- /mosdef_gomc/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GOMC-WSU/MoSDeF-GOMC/4b50913a5c25e9eb6b4ba76d9b1ca364b8b65197/mosdef_gomc/tests/__init__.py -------------------------------------------------------------------------------- /mosdef_gomc/utils/__init__.py: -------------------------------------------------------------------------------- 1 | """mosdef_gomc utilities.""" 2 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/2_ethane.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ETH 3 | 16 14 1 0 0 4 | SMALL 5 | USER_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 C1 35.5140 19.2460 34.4170 C 1 ETH -0.180000 11 | 2 C2 36.6600 18.6240 33.6370 C 1 ETH -0.180000 12 | 3 H3 35.4340 20.3260 34.1710 H 1 ETH 0.060000 13 | 4 H4 34.5610 18.7410 34.1540 H 1 ETH 0.060000 14 | 5 H5 35.6970 19.1340 35.5070 H 1 ETH 0.060000 15 | 6 H6 37.6130 19.1290 33.8990 H 1 ETH 0.060000 16 | 7 H7 36.7400 17.5440 33.8830 H 1 ETH 0.060000 17 | 8 H8 36.4770 18.7350 32.5470 H 1 ETH 0.060000 18 | 9 C8 29.0900 26.1850 32.0230 C 2 ETH -0.180000 19 | 10 C9 27.9240 27.0340 31.5460 C 2 ETH -0.180000 20 | 11 H10 30.0320 26.7690 31.9580 H 2 ETH 0.060000 21 | 12 H11 28.9240 25.8760 33.0760 H 2 ETH 0.060000 22 | 13 H12 29.1790 25.2790 31.3870 H 2 ETH 0.060000 23 | 14 H13 28.0890 27.3430 30.4920 H 2 ETH 0.060000 24 | 15 H14 26.9810 26.4500 31.6110 H 2 ETH 0.060000 25 | 16 H15 27.8340 27.9410 32.1810 H 2 ETH 0.060000 26 | @BOND 27 | 1 1 2 1 28 | 2 1 3 1 29 | 3 1 4 1 30 | 4 1 5 1 31 | 5 2 6 1 32 | 6 2 7 1 33 | 7 2 8 1 34 | 8 9 10 1 35 | 9 9 11 1 36 | 10 9 12 1 37 | 11 9 13 1 38 | 12 10 14 1 39 | 13 10 15 1 40 | 14 10 16 1 41 | 42 | @SUBSTRUCTURE 43 | 1 **** 1 TEMP 0 **** **** 0 ROOT 44 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/Charmm_writer_testing_only_zeolite.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/ETV_triclinic.cif: -------------------------------------------------------------------------------- 1 | data_ETV 2 | 3 | 4 | #************************************************************************** 5 | # 6 | # CIF taken from the IZA-SC Database of Zeolite Structures 7 | # Ch. Baerlocher and L.B. McCusker 8 | # Database of Zeolite Structures: http://www.iza-structure.org/databases/ 9 | # 10 | # The atom coordinates and the cell parameters were optimized with DLS76 11 | # assuming a pure SiO2 composition. 12 | # 13 | #************************************************************************** 14 | 15 | 16 | _cell_length_a 8.7503 17 | _cell_length_b 9.6479 18 | _cell_length_c 10.2719 19 | _cell_angle_alpha 105.7200 20 | _cell_angle_beta 100.1900 21 | _cell_angle_gamma 97.0200 22 | 23 | _symmetry_space_group_name_H-M 'P -1' 24 | _symmetry_Int_Tables_number 2 25 | _symmetry_cell_setting triclinic 26 | 27 | 28 | loop_ 29 | _symmetry_equiv_pos_as_xyz 30 | '+x,+y,+z' 31 | '-x,-y,-z' 32 | 33 | loop_ 34 | _atom_site_label 35 | _atom_site_type_symbol 36 | _atom_site_fract_x 37 | _atom_site_fract_y 38 | _atom_site_fract_z 39 | Si1 Si 0.5462 0.3074 0.1830 40 | Si2 Si 0.5543 0.3985 0.8022 41 | Si3 Si 0.5720 0.0660 0.3233 42 | Si4 Si 0.3062 0.8514 0.3594 43 | Si5 Si 0.3282 0.1836 0.8867 44 | Si6 Si 0.9955 0.7220 0.1426 45 | Si7 Si 0.8127 0.4160 0.0600 46 | O1 O 0.5550 0.2212 0.2975 47 | O2 O 0.6888 0.4517 0.9431 48 | O3 O 0.3997 0.9766 0.3116 49 | O4 O 0.3997 0.3095 0.8273 50 | O5 O 0.4226 0.2094 0.0432 51 | O6 O 0.1229 0.8156 0.2817 52 | O7 O 0.4897 0.4606 0.2413 53 | O8 O 0.7183 0.3390 0.1504 54 | O9 O 0.1446 0.1887 0.8848 55 | O10 O 0.6790 0.0928 0.4756 56 | O11 O 0.6549 0.9739 0.2089 57 | O12 O 0.3816 0.7055 0.3195 58 | O13 O 0.9234 0.5671 0.1585 59 | O14 O 0.9196 0.3078 0.9867 60 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/benzene_GAFF.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 2 62 | 63 | 64 | 15.167 65 | 66 | 67 | 3.141592653589793 68 | 69 | 70 | 71 | 72 | 73 | 74 | 2 75 | 76 | 77 | 4.6024 78 | 79 | 80 | 3.141592653589793 81 | 82 | 83 | 84 | 85 | 86 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/benzene_aa.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | BEN 3 | 12 12 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 C 0.0000 0.0000 0.0000 C 1 BEN 0.000000 11 | 2 C 1.4000 0.0000 0.0000 C 1 BEN 0.000000 12 | 3 C 2.1000 1.2124 0.0000 C 1 BEN 0.000000 13 | 4 C 1.4000 2.4249 0.0000 C 1 BEN 0.000000 14 | 5 C 0.0000 2.4249 0.0000 C 1 BEN 0.000000 15 | 6 C -0.7000 1.2124 0.0000 C 1 BEN 0.000000 16 | 7 H -0.5000 -0.8660 0.0000 H 1 BEN 0.000000 17 | 8 H 1.9000 -0.8660 0.0000 H 1 BEN 0.000000 18 | 9 H 3.1000 1.2124 0.0000 H 1 BEN 0.000000 19 | 10 H 1.9000 3.2909 0.0000 H 1 BEN 0.000000 20 | 11 H -0.5000 3.2909 0.0000 H 1 BEN 0.000000 21 | 12 H -1.7000 1.2124 0.0000 H 1 BEN 0.000000 22 | @BOND 23 | 1 1 2 2 24 | 2 1 6 1 25 | 3 1 7 1 26 | 4 2 3 1 27 | 5 2 8 1 28 | 6 3 4 2 29 | 7 3 9 1 30 | 8 4 5 1 31 | 9 4 10 1 32 | 10 5 6 2 33 | 11 5 11 1 34 | 12 6 12 1 35 | 36 | @SUBSTRUCTURE 37 | 1 **** 1 TEMP 0 **** **** 0 ROOT 38 | 39 | #generated by VMD 40 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/benzene_and_alkane_branched_benzene_aa.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/butane_aa.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | BUT 3 | 14 13 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 C1 -2.2000 1.2124 0.0000 C 1 BUT 0.000000 11 | 2 C2 -1.5000 0.0000 0.0000 C 1 BUT 0.000000 12 | 3 C3 0.0000 0.0000 0.0000 C 1 BUT 0.000000 13 | 4 C4 0.7000 -1.2124 -0.0000 C 1 BUT 0.000000 14 | 5 H41 1.6803 -1.0254 -0.1206 H 1 BUT 0.000000 15 | 6 H11 -1.8131 1.7905 0.7126 H 1 BUT 0.000000 16 | 7 H12 -1.9666 1.7544 -0.8134 H 1 BUT 0.000000 17 | 8 H21 -1.8198 -0.4847 -0.8141 H 1 BUT 0.000000 18 | 9 H22 -1.8198 -0.4847 0.8141 H 1 BUT 0.000000 19 | 10 H13 -3.1971 1.2516 0.0959 H 1 BUT 0.000000 20 | 11 H42 0.5936 -1.5578 0.9099 H 1 BUT 0.000000 21 | 12 H43 0.3070 -1.8446 -0.4962 H 1 BUT 0.000000 22 | 13 H31 0.2177 0.2554 -0.8800 H 1 BUT 0.000000 23 | 14 H32 0.4042 0.6781 0.5034 H 1 BUT 0.000000 24 | @BOND 25 | 1 3 2 1 26 | 2 3 4 1 27 | 3 3 13 1 28 | 4 3 14 1 29 | 5 2 1 1 30 | 6 2 8 1 31 | 7 2 9 1 32 | 8 1 6 1 33 | 9 1 7 1 34 | 10 1 10 1 35 | 11 4 5 1 36 | 12 4 11 1 37 | 13 4 12 1 38 | 39 | @SUBSTRUCTURE 40 | 1 **** 1 TEMP 0 **** **** 0 ROOT 41 | 42 | #generated by VMD 43 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/charmm_mie_ff_file_test_single_bonds_angles_dihedrals_impropers_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/charmm_psf_6_char_atom_names_test_single_bonds_angles_dihedrals_impropers_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/charmm_psf_7_char_atom_names_test_single_bonds_angles_dihedrals_impropers_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/charmm_psf_test_single_bonds_angles_dihedrals_impropers_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/ethane_propane_ua_Mie_lorentz_combining.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/ethane_propane_ua_bad_eqn_lorentz_combining.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/ethane_propane_ua_lorentz_combining.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/ethane_ua.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ETH 3 | 2 1 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 _CH3 0.0000 0.0000 0.0000 C 1 ETH 0.000000 11 | 2 _CH3 1.5400 0.0000 0.0000 C 1 ETH 0.000000 12 | @BOND 13 | 1 1 2 1 14 | 15 | @SUBSTRUCTURE 16 | 1 **** 1 TEMP 0 **** **** 0 ROOT 17 | 18 | #generated by VMD 19 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/ethane_ua_mie.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ETHM 3 | 2 1 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 _CH3 0.0000 0.0000 0.0000 C 1 ETHM 0.000000 11 | 2 _CH3 1.5400 0.0000 0.0000 C 1 ETHM 0.000000 12 | @BOND 13 | 1 1 2 1 14 | 15 | @SUBSTRUCTURE 16 | 1 **** 1 TEMP 0 **** **** 0 ROOT 17 | 18 | #generated by VMD 19 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/ethyl_benzene_aa.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | EBN 3 | 18 18 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 C 0.0000 0.0000 0.0000 C 1 EBN 0.000000 11 | 2 C 1.4000 0.0000 0.0000 C 1 EBN 0.000000 12 | 3 C 2.1000 1.2124 0.0000 C 1 EBN 0.000000 13 | 4 C 1.4000 2.4249 0.0000 C 1 EBN 0.000000 14 | 5 C 0.0000 2.4249 0.0000 C 1 EBN 0.000000 15 | 6 C -0.7000 1.2124 0.0000 C 1 EBN 0.000000 16 | 7 C -2.2000 1.2123 0.0000 C 1 EBN 0.000000 17 | 8 C -2.9501 2.5113 0.0000 C 1 EBN 0.000000 18 | 9 H -0.5000 -0.8660 0.0000 H 1 EBN 0.000000 19 | 10 H 1.9000 -0.8660 0.0000 H 1 EBN 0.000000 20 | 11 H 3.1000 1.2123 0.0000 H 1 EBN 0.000000 21 | 12 H 1.9000 3.2909 0.0000 H 1 EBN 0.000000 22 | 13 H -0.5000 3.2909 0.0000 H 1 EBN 0.000000 23 | 14 H -2.4903 0.7094 -0.8141 H 1 EBN 0.000000 24 | 15 H -2.4903 0.7094 0.8141 H 1 EBN 0.000000 25 | 16 H -2.2941 3.2660 -0.0000 H 1 EBN 0.000000 26 | 17 H -3.5223 2.5568 -0.8188 H 1 EBN 0.000000 27 | 18 H -3.5223 2.5568 0.8188 H 1 EBN 0.000000 28 | @BOND 29 | 1 1 2 1 30 | 2 1 6 2 31 | 3 1 9 1 32 | 4 2 3 2 33 | 5 2 10 1 34 | 6 3 4 1 35 | 7 3 11 1 36 | 8 4 5 2 37 | 9 4 12 1 38 | 10 5 6 1 39 | 11 5 13 1 40 | 12 6 7 1 41 | 13 7 8 1 42 | 14 7 14 1 43 | 15 7 15 1 44 | 16 8 16 1 45 | 17 8 17 1 46 | 18 8 18 1 47 | 48 | @SUBSTRUCTURE 49 | 1 **** 1 TEMP 0 **** **** 0 ROOT 50 | 51 | #generated by VMD 52 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_benzene_GAFF.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 2 62 | 63 | 64 | 15.167 65 | 66 | 67 | 3.141592653589793 68 | 69 | 70 | 71 | 72 | 73 | 74 | 2 75 | 76 | 77 | 4.6024 78 | 79 | 80 | 3.141592653589793 81 | 82 | 83 | 84 | 85 | 86 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_hexane_Exp6_eqn_times_2_periodic_dihedral_ua_K_energy.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_hexane_Exp6_periodic_dihedral_ua_K_energy_units.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_spce_water_LJ_eqn_times_2_one_for_nb_and_coul__lorentz_combining.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_spce_water__geometric_combining.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_spce_water__lorentz_combining.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_spce_water__no_combining_rule.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_spce_water_bad_charges__lorentz_combining.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_spce_water_half_for_nb__half_coul__lorentz_combining.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_spce_water_one_for_nb_and_coul__lorentz_combining.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_spce_water_zero_for_nb__half_coul__lorentz_combining.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_spce_water_zero_for_nb_and_coul__geometric_combining.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_Mie_OPLS_dihedral_ua_K_energy_units.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_Mie_RB_dihedral_ua_K_energy_units.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_OPLS_dihedrals_0_5_times_1_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_OPLS_dihedrals_0_5_times_2_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_OPLS_dihedrals_half_times_1_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_OPLS_dihedrals_half_times_2_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_RB_dihedrals_times_1_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_RB_dihedrals_times_2_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_RB_dihedrals_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_bad_form_angles_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 0 86 | 1 87 | 2 88 | 3 89 | 4 90 | 91 | 92 | 2.70802 93 | -1.6406925 94 | -0.261575 95 | 1.4460525 96 | 0 97 | 98 | 99 | 90 100 | 180 101 | 0 102 | 180 103 | 0 104 | 105 | 106 | 107 | 108 | 109 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_bad_form_bonds_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 0 86 | 1 87 | 2 88 | 3 89 | 4 90 | 91 | 92 | 2.70802 93 | -1.6406925 94 | -0.261575 95 | 1.4460525 96 | 0 97 | 98 | 99 | 90 100 | 180 101 | 0 102 | 180 103 | 0 104 | 105 | 106 | 107 | 108 | 109 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_bad_form_dihedrals_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_harmonic_dihedrals_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_periodic_dihedrals_ua_all_bond_angles_dihedrals_k_times_1.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 0 86 | 1 87 | 2 88 | 3 89 | 90 | 91 | 2.70802 92 | -1.6406925 93 | -0.261575 94 | 1.4460525 95 | 96 | 97 | 1.570796326794897 98 | 3.141592653589793 99 | 0.0 100 | 3.141592653589793 101 | 102 | 103 | 104 | 105 | 106 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_periodic_dihedrals_ua_all_bond_angles_dihedrals_k_times_half.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 0 86 | 1 87 | 2 88 | 3 89 | 90 | 91 | 2.70802 92 | -1.6406925 93 | -0.261575 94 | 1.4460525 95 | 96 | 97 | 1.570796326794897 98 | 3.141592653589793 99 | 0.0 100 | 3.141592653589793 101 | 102 | 103 | 104 | 105 | 106 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/gmso_two_propanol_periodic_wildcard_dihedrals_ua.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 0 86 | 1 87 | 2 88 | 3 89 | 90 | 91 | 2.70802 92 | -1.6406925 93 | -0.261575 94 | 1.4460525 95 | 96 | 97 | 1.570796326794897 98 | 3.141592653589793 99 | 0.0 100 | 3.141592653589793 101 | 102 | 103 | 104 | 105 | 106 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/hexane_ua.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | HEX 3 | 6 5 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 _CH3 0.0000 0.0000 0.0000 C 1 HEX 0.000000 11 | 2 _CH2 -1.5000 0.0000 0.0000 C 1 HEX 0.000000 12 | 3 _CH2 -2.2500 1.2990 0.0000 C 1 HEX 0.000000 13 | 4 _CH2 -2.3176 2.1344 1.2440 C 1 HEX 0.000000 14 | 5 _CH2 -2.4830 1.4760 2.5816 C 1 HEX 0.000000 15 | 6 _CH3 -2.1676 0.0185 2.7441 C 1 HEX 0.000000 16 | @BOND 17 | 1 1 2 1 18 | 2 2 3 1 19 | 3 3 4 1 20 | 4 4 5 1 21 | 5 5 6 1 22 | 23 | @SUBSTRUCTURE 24 | 1 **** 1 TEMP 0 **** **** 0 ROOT 25 | 26 | #generated by VMD 27 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/methyl_benzene_aa.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MBN 3 | 15 15 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 C 0.0000 0.0000 0.0000 C 1 MBN 0.000000 11 | 2 C 1.4000 0.0000 0.0000 C 1 MBN 0.000000 12 | 3 C 2.1000 1.2124 0.0000 C 1 MBN 0.000000 13 | 4 C 1.4000 2.4249 0.0000 C 1 MBN 0.000000 14 | 5 C 0.0000 2.4249 0.0000 C 1 MBN 0.000000 15 | 6 C -0.7000 1.2124 0.0000 C 1 MBN 0.000000 16 | 7 C -2.2000 1.2123 0.0000 C 1 MBN 0.000000 17 | 8 H -0.5000 -0.8660 0.0000 H 1 MBN 0.000000 18 | 9 H 1.9000 -0.8660 0.0000 H 1 MBN 0.000000 19 | 10 H 3.1000 1.2123 0.0000 H 1 MBN 0.000000 20 | 11 H 1.9000 3.2909 0.0000 H 1 MBN 0.000000 21 | 12 H -0.5000 3.2909 0.0000 H 1 MBN 0.000000 22 | 13 H -2.5255 0.2668 0.0000 H 1 MBN 0.000000 23 | 14 H -2.5256 1.6850 0.8188 H 1 MBN 0.000000 24 | 15 H -2.5256 1.6850 -0.8188 H 1 MBN 0.000000 25 | @BOND 26 | 1 1 2 1 27 | 2 1 6 2 28 | 3 1 8 1 29 | 4 2 3 2 30 | 5 2 9 1 31 | 6 3 4 1 32 | 7 3 10 1 33 | 8 4 5 2 34 | 9 4 11 1 35 | 10 5 6 1 36 | 11 5 12 1 37 | 12 6 7 1 38 | 13 7 13 1 39 | 14 7 14 1 40 | 15 7 15 1 41 | 42 | @SUBSTRUCTURE 43 | 1 **** 1 TEMP 0 **** **** 0 ROOT 44 | 45 | #generated by VMD 46 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/propane_ua.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | PRO 3 | 3 2 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 _CH3 0.0000 0.0000 0.0000 C 1 PRO 0.000000 11 | 2 _CH2 1.5400 0.0000 0.0000 C 1 PRO 0.000000 12 | 3 _CH3 3.0800 0.0000 0.0000 C 1 PRO 0.000000 13 | @BOND 14 | 1 1 2 1 15 | 2 2 3 1 16 | 17 | @SUBSTRUCTURE 18 | 1 **** 1 TEMP 0 **** **** 0 ROOT 19 | 20 | #generated by VMD 21 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/psf_file_single_angle_test_ua.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MOL 3 | 3 2 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 _BD 0.0000 0.0000 0.0000 C 1 MOL 0.000000 11 | 2 _BD -1.5000 0.0000 0.0000 C 1 MOL 0.000000 12 | 3 _BD -2.2500 1.2990 0.0000 C 1 MOL 0.000000 13 | @BOND 14 | 1 1 2 1 15 | 2 2 3 1 16 | 17 | @SUBSTRUCTURE 18 | 1 **** 1 TEMP 0 **** **** 0 ROOT 19 | 20 | #generated by VMD 21 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/psf_file_single_bond_test_ua.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MOL 3 | 2 1 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 _BD 0.0000 0.0000 0.0000 C 1 MOL 0.000000 11 | 2 _BD -1.5000 0.0000 0.0000 C 1 MOL 0.000000 12 | @BOND 13 | 1 1 2 1 14 | 15 | @SUBSTRUCTURE 16 | 1 **** 1 TEMP 0 **** **** 0 ROOT 17 | 18 | #generated by VMD 19 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/psf_file_single_dihedral_test_ua.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MOL 3 | 4 3 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 _BD 0.0000 0.0000 0.0000 C 1 MOL 0.000000 11 | 2 _BD -1.5000 0.0000 0.0000 C 1 MOL 0.000000 12 | 3 _BD -2.2500 1.2990 0.0000 C 1 MOL 0.000000 13 | 4 _BD -2.9405 1.7775 -1.2427 C 1 MOL 0.000000 14 | @BOND 15 | 1 1 2 1 16 | 2 2 3 1 17 | 3 3 4 1 18 | 19 | @SUBSTRUCTURE 20 | 1 **** 1 TEMP 0 **** **** 0 ROOT 21 | 22 | #generated by VMD 23 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/psf_file_single_improper_test_ua.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MOL 3 | 7 6 1 0 0 4 | SMALL 5 | NO_CHARGES 6 | **** 7 | Energy = 0 8 | 9 | @ATOM 10 | 1 _BD 0.0000 0.0000 0.0000 C 1 MOL 0.000000 11 | 2 _BD -1.5000 0.0000 0.0000 C 1 MOL 0.000000 12 | 3 _BD 0.7500 -1.2990 -0.0000 C 1 MOL 0.000000 13 | 4 _BD 0.7500 1.2990 0.0000 C 1 MOL 0.000000 14 | 5 _XB 1.4372 1.7685 -1.2479 C 1 MOL 0.000000 15 | 6 _XB 0.8418 2.8812 -2.0586 C 1 MOL 0.000000 16 | 7 _XB 2.7198 1.1253 -1.6851 C 1 MOL 0.000000 17 | @BOND 18 | 1 1 2 1 19 | 2 1 3 1 20 | 3 1 4 2 21 | 4 4 5 1 22 | 5 5 6 1 23 | 6 5 7 1 24 | 25 | @SUBSTRUCTURE 26 | 1 **** 1 TEMP 0 **** **** 0 ROOT 27 | 28 | #generated by VMD 29 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/files/spce_coul_14_half__LJ_14_zero.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /mosdef_gomc/utils/io.py: -------------------------------------------------------------------------------- 1 | """General module for IO operations in MOSDEF-GOMC.""" 2 | 3 | import os 4 | 5 | from pkg_resources import resource_filename 6 | 7 | 8 | def get_mosdef_gomc_fn(filename): 9 | """Get the full path to one of the reference files shipped for utils. 10 | In the source distribution, these files are in ``mosdef_gomc/utils/files``, 11 | but on installation, they're moved to somewhere in the user's python 12 | site-packages directory. 13 | Parameters 14 | ---------- 15 | filename : str 16 | Name of the file to load (with respect to the files/ folder). 17 | Returns 18 | ------- 19 | fn : str 20 | Full path to filename 21 | """ 22 | fn = resource_filename( 23 | "mosdef_gomc", os.path.join("utils", "files", filename) 24 | ) 25 | if not os.path.exists(fn): 26 | raise IOError("Sorry! {} does not exists.".format(fn)) 27 | return fn 28 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [bumpversion] 2 | current_version = 1.4.0 3 | commit = True 4 | tag = True 5 | message = Bump to version {new_version} 6 | tag_name = {new_version} 7 | 8 | [coverage:run] 9 | omit = 10 | mosdef_gomc/tests/* 11 | 12 | [coverage:report] 13 | exclude_lines = 14 | pragma: no cover 15 | 16 | if 0: 17 | if __name__ == .__main__.: 18 | def __repr__ 19 | except ImportError 20 | omit = 21 | mosdef_gomc/tests/* 22 | 23 | [bumpversion:file:mosdef_gomc/__init__.py] 24 | 25 | [bumpversion:file:setup.py] 26 | 27 | [bumpversion:file:docs/conf.py] 28 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | """ 2 | MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC 3 | """ 4 | 5 | import os 6 | import subprocess 7 | from distutils.spawn import find_executable 8 | 9 | from setuptools import find_packages, setup 10 | 11 | ######################################### 12 | NAME = "MoSDeF-GOMC" 13 | VERSION = "1.4.0" 14 | ISRELEASED = True 15 | if ISRELEASED: 16 | __version__ = VERSION 17 | else: 18 | __version__ = VERSION + ".dev0" 19 | ######################################### 20 | 21 | 22 | def proto_procedure(): 23 | # Find the Protocol Compiler and compile protocol buffers 24 | # Only compile if a protocompiler is found, otherwise don't do anything 25 | if "PROTOC" in os.environ and os.path.exists(os.environ["PROTOC"]): 26 | protoc = os.environ["PROTOC"] 27 | elif os.path.exists("../src/protoc"): 28 | protoc = "../src/protoc" 29 | elif os.path.exists("../src/protoc.exe"): 30 | protoc = "../src/protoc.exe" 31 | elif os.path.exists("../vsprojects/Debug/protoc.exe"): 32 | protoc = "../vsprojects/Debug/protoc.exe" 33 | elif os.path.exists("../vsprojects/Release/protoc.exe"): 34 | protoc = "../vsprojects/Release/protoc.exe" 35 | else: 36 | protoc = find_executable("protoc") 37 | if protoc is None: 38 | protoc = find_executable("protoc.exe") 39 | 40 | if protoc is not None: 41 | compile_proto(protoc) 42 | 43 | 44 | def compile_proto(protoc): 45 | protoc_command = [ 46 | protoc, 47 | "-I=mosdef_gomc/formats/", 48 | "--python_out=mosdef_gomc/formats/", 49 | "compound.proto", 50 | ] 51 | subprocess.call(protoc_command) 52 | 53 | 54 | if __name__ == "__main__": 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/MoSDeF-GOMC", 65 | download_url="https://github.com/GOMC-WSU/MoSDeF-GOMC/tarball/{}".format( 66 | __version__ 67 | ), 68 | packages=find_packages(), 69 | package_data={ 70 | "MoSDeF-GOMC": [ 71 | "utils/reference/*.{pdb,mol2}", 72 | "lib/*.{pdb,mol2}", 73 | ] 74 | }, 75 | package_dir={"MoSDeF-GOMC": "MoSDeF-GOMC"}, 76 | include_package_data=True, 77 | license="MIT", 78 | zip_safe=False, 79 | keywords="MoSDeF-GOMC", 80 | classifiers=[ 81 | "Development Status :: 0 - 1", 82 | "Intended Audience :: Science/Research", 83 | "Intended Audience :: Developers", 84 | "License :: OSI Approved :: MIT 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 | --------------------------------------------------------------------------------