├── .DS_Store ├── ClayFF.ff ├── ffbonded.itp ├── ffnonbonded.itp ├── forcefield.itp ├── ions.itp ├── spc.itp └── spce.itp ├── README.md ├── examples ├── montmorrilonite │ ├── MontARUC.gro │ ├── ffMontAR.itp │ └── topol.top └── pyrophyllite │ ├── PyroUnitCell.gro │ ├── ffPyroUC.itp │ └── topol.top ├── media ├── image1.png ├── image2.png ├── image3.png ├── image4.png └── image5.png └── tutorial ├── .DS_Store ├── GROMACS_tutorial.docx └── clayFF_example ├── 00_setup ├── ClayFF.ff │ ├── atomtypes.atp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ └── spc.itp ├── PyroUnitCell.gro ├── ffPyroUC.itp └── topol.top ├── 01_min └── energy_min.mdp ├── 02_eqm └── equil_md.mdp └── 03_prod └── prod_md.mdp /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomasunderwood/ClayFF/137ea3256db2a3c66f90f834084772aa406e90ad/.DS_Store -------------------------------------------------------------------------------- /ClayFF.ff/ffbonded.itp: -------------------------------------------------------------------------------- 1 | 2 | [ bondtypes ] 3 | o* h* 1 0.1 463700 4 | ho oh 1 0.1 463700 5 | ho ohs 1 0.1 463700 6 | 7 | [ angletypes ] 8 | h* o* h* 1 109.47 383.00 9 | ao oh ho 1 109.47 251.04 10 | ao ohs ho 1 109.47 251.04 11 | at oh ho 1 109.47 251.04 12 | at ohs ho 1 109.47 251.04 13 | mgh oh ho 1 109.47 251.04 14 | mgh ohs ho 1 109.47 251.04 15 | cah oh ho 1 109.47 251.04 16 | cah ohs ho 1 109.47 251.04 17 | feo oh ho 1 109.47 251.04 18 | feo ohs ho 1 109.47 251.04 19 | lio oh ho 1 109.47 251.04 20 | lio ohs ho 1 109.47 251.04 -------------------------------------------------------------------------------- /ClayFF.ff/ffnonbonded.itp: -------------------------------------------------------------------------------- 1 | ;; charges are / can be overwritten later in .itp files 2 | 3 | [ atomtypes ] 4 | ;; name at.num mass charge ptype sigma epsilon 5 | h* 1 1.0079 0.41 A 0.000000 0.000000 ; h* water hydrogen 6 | ho 1 1.0079 0.425 A 0.000000 0.000000 ; ho hydroxyl hydrogen 7 | o* 8 15.9994 -0.82 A 0.316554 0.650194 ; o* water oxygen 8 | oh 8 15.9994 -0.95 A 0.316554 0.650194 ; oh hydroxyl oxygen 9 | ob 8 15.9994 -1.05 A 0.316554 0.650194 ; ob bridging oxygen 10 | obos 8 15.9994 -1.1808 A 0.316554 0.650194 ; obos bridging oxygen with octahedral substitution 11 | obts 8 15.9994 -1.1688 A 0.316554 0.650194 ; obts bridging oxygen with tetrahedral substitution 12 | obss 8 15.9994 -1.2996 A 0.316554 0.650194 ; obss bridging oxygen with double substitution 13 | ohs 8 15.9994 -1.0808 A 0.316554 0.650194 ; ohs hydroxyl oxygen with substitution 14 | st 14 28.0855 2.1 A 0.330203 7.70065E-06 ; st tetrahedral silicon 15 | ao 13 26.981538 1.575 A 0.427124 5.56388E-06 ; ao octahedral aluminum 16 | at 13 26.981538 1.575 A 0.330203 7.70065E-06 ; at tetrahedral aluminum 17 | mgo 12 24.305 1.36 A 0.526432 3.77807E-06 ; mgo octahedral magnesium 18 | mgh 12 24.305 1.05 A 0.526432 3.77807E-06 ; mgh hydroxide magnesium 19 | cao 20 40.078 1.36 A 0.556669 2.10447E-05 ; cao octahedral calcium 20 | cah 20 40.078 1.05 A 0.556170 2.10447E-05 ; cah hydroxide calcium 21 | feo 26 55.845 1.575 A 0.490618 3.77807E-06 ; feo octahedral iron (n.b. epsilon corrected over original publication) 22 | lio 3 6.941 0.525 A 0.421012 3.77807E-05 ; lio octahedral lithium 23 | 24 | ; Original ion parameters in ClayFF 25 | ;; name at.num mass charge ptype sigma epsilon 26 | Na 11 22.98977 1 A 0.004187 0.544338 ; Na aqueous sodium ion 27 | K 19 39.0983 1 A 0.004187 0.418400 ; K aqueous potassium ion 28 | Cs 55 132.90545 1 A 0.383104 0.418400 ; Cs aqueous cesium ion 29 | Ca 20 40.078 2 A 0.287199 0.418400 ; Ca aqueous calcium ion 30 | Ba 56 137.327 2 A 0.381661 0.196648 ; Ba aqueous barium ion 31 | Cl 17 35.453 -1 A 0.439997 0.418818 ; Cl aqueous chloride ion 32 | 33 | #ifdef JoungCheatham 34 | ; Joung Cheatham 2008 (Same for SPC and SPC/E) 35 | ;; name at.num mass charge ptype sigma epsilon 36 | Li 3 6.941000 1 A 0.140940 1.40890 ; Aqueous lithium ion 37 | Na 11 22.98977 1 A 0.215954 1.47545 ; Aqueous sodium ion 38 | K 19 39.09830 1 A 0.283840 1.79789 ; Aqueous potassium ion 39 | Rb 37 85.46783 1 A 0.309498 1.8623 ; Aqueous rubinium ion 40 | Cs 55 132.9055 1 A 0.360100 0.37596 ; Aqueous cesium ion 41 | F 9 18.99840 -1 A 0.402152 0.000321 ; Aqueous fluoride ion 42 | Cl 17 35.45300 -1 A 0.483050 0.05349 ; Aqueous chloride ion 43 | Br 35 79.90400 -1 A 0.490170 0.11279 ; Aqueous bromide ion 44 | I 53 126.9045 -1 A 0.520107 0.17901 ; Aqueous iodide ion 45 | Ca 20 40.07800 2 A 0.291324 0.409530 ; (CM) P Li, B P. Roberts, D K. Chakravorty, and K M. Merz 46 | #endif 47 | 48 | ; Define the atomtypes for the different water models 49 | ; SPC water 50 | ;; name at.num mass charge ptype sigma epsilon 51 | HW_spc 1 1.0079 0.41 A 0.000000 0.000000 ; SPC water hydrogen 52 | OW_spc 8 15.9994 -0.82 A 0.316554 0.650194 ; SPC water oxygen 53 | ; SPC/E water 54 | ;; name at.num mass charge ptype sigma epsilon 55 | HW_spce 1 1.0079 0.4238 A 0.000000 0.000000 ; SPC/E water hydrogen 56 | OW_spce 8 15.9994 -0.8476 A 0.316554 0.650194 ; SPC/E water oxygen 57 | -------------------------------------------------------------------------------- /ClayFF.ff/forcefield.itp: -------------------------------------------------------------------------------- 1 | ; The ClayFF forcefield. 2 | ; 3 | ; References 4 | ; 5 | ; R.T Cygan, J.J Liang, A.G. Kalinichev, J. Phys. Chem. B, 2004, 108 (4), pp 1255–1266 6 | ; http://dx.doi.org/10.1021/jp0363287 7 | 8 | ; nbfunc 1 == Lennard-Jones formula for non-bonded interactions 9 | ; comb-rule 2 == Lorentz-Berthelot mixing rules 10 | 11 | [ defaults ] 12 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 13 | 1 2 yes 1.0 1.0 14 | 15 | #include "ffnonbonded.itp" 16 | #include "ffbonded.itp" 17 | -------------------------------------------------------------------------------- /ClayFF.ff/ions.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | Na 1 4 | 5 | [ atoms ] 6 | ; id at type res nr residu name at name cg nr charge 7 | 1 Na 1 Na Na 1 1 8 | 9 | [ moleculetype ] 10 | ; molname nrexcl 11 | K 1 12 | 13 | [ atoms ] 14 | ; id at type res nr residu name at name cg nr charge 15 | 1 K 1 K K 1 1 16 | 17 | [ moleculetype ] 18 | ; molname nrexcl 19 | Cs 1 20 | 21 | [ atoms ] 22 | ; id at type res nr residu name at name cg nr charge 23 | 1 Cs 1 Cs Cs 1 1 24 | 25 | [ moleculetype ] 26 | ; molname nrexcl 27 | Ca 1 28 | 29 | [ atoms ] 30 | ; id at type res nr residu name at name cg nr charge 31 | 1 Ca 1 Ca Ca 1 2 32 | 33 | [ moleculetype ] 34 | ; molname nrexcl 35 | Ba 1 36 | 37 | [ atoms ] 38 | ; id at type res nr residu name at name cg nr charge 39 | 1 Ba 1 Ba Ba 1 2 40 | 41 | [ moleculetype ] 42 | ; molname nrexcl 43 | Cl 1 44 | 45 | 46 | [ atoms ] 47 | ; id at type res nr residu name at name cg nr charge 48 | 1 Cl 1 Cl Cl 1 -1 49 | 50 | #ifdef JoungCheatham 51 | [ moleculetype ] 52 | ; molname nrexcl 53 | Li 1 54 | 55 | [ atoms ] 56 | ; id at type res nr residu name at name cg nr charge 57 | 1 Li 1 Li Li 1 1 58 | 59 | [ moleculetype ] 60 | ; molname nrexcl 61 | Rb 1 62 | 63 | [ atoms ] 64 | ; id at type res nr residu name at name cg nr charge 65 | 1 Rb 1 Rb Rb 1 1 66 | 67 | [ moleculetype ] 68 | ; molname nrexcl 69 | F 1 70 | 71 | [ atoms ] 72 | ; id at type res nr residu name at name cg nr charge 73 | 1 F 1 F F 1 -1 74 | 75 | [ moleculetype ] 76 | ; molname nrexcl 77 | Br 1 78 | 79 | [ atoms ] 80 | ; id at type res nr residu name at name cg nr charge 81 | 1 Br 1 Br Br 1 -1 82 | 83 | [ moleculetype ] 84 | ; molname nrexcl 85 | I 1 86 | 87 | [ atoms ] 88 | ; id at type res nr residu name at name cg nr charge 89 | 1 I 1 I I 1 -1 90 | #endif -------------------------------------------------------------------------------- /ClayFF.ff/spc.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | SOL 2 4 | 5 | [ atoms ] 6 | ; nr type resnr residue atom cgnr charge mass 7 | #ifndef HEAVY_H 8 | 1 OW_spc 1 SOL OW 1 -0.82 15.99940 9 | 2 HW_spc 1 SOL HW1 1 0.41 1.00800 10 | 3 HW_spc 1 SOL HW2 1 0.41 1.00800 11 | #else 12 | 1 OW_spc 1 SOL OW 1 -0.82 9.95140 13 | 2 HW_spc 1 SOL HW1 1 0.41 4.03200 14 | 3 HW_spc 1 SOL HW2 1 0.41 4.03200 15 | #endif 16 | 17 | #ifndef FLEXIBLE 18 | [ settles ] 19 | ; OW funct doh dhh 20 | 1 1 0.1 0.16330 21 | 22 | [ exclusions ] 23 | 1 2 3 24 | 2 1 3 25 | 3 1 2 26 | 27 | #else 28 | [ bonds ] 29 | ; i j funct length force.c. 30 | 1 2 1 0.1 463700 31 | 1 3 1 0.1 463700 32 | 33 | [ angles ] 34 | ; i j k funct angle force.c. 35 | 2 1 3 1 109.47 383 109.47 383 36 | #endif 37 | -------------------------------------------------------------------------------- /ClayFF.ff/spce.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | SOL 2 4 | 5 | [ atoms ] 6 | ; nr type resnr residue atom cgnr charge mass 7 | #ifndef HEAVY_H 8 | 1 OW_spce 1 SOL OW 1 -0.8476 15.9994 9 | 2 HW_spce 1 SOL HW1 1 0.4238 1.00794 10 | 3 HW_spce 1 SOL HW2 1 0.4238 1.00794 11 | #else 12 | 1 OW_spce 1 SOL OW 1 -0.8476 9.95140 13 | 2 HW_spce 1 SOL HW1 1 0.4238 4.03200 14 | 3 HW_spce 1 SOL HW2 1 0.4238 4.03200 15 | #endif 16 | 17 | #ifndef FLEXIBLE 18 | [ settles ] 19 | ; OW funct doh dhh 20 | 1 1 0.1 0.16330 21 | 22 | [ exclusions ] 23 | 1 2 3 24 | 2 1 3 25 | 3 1 2 26 | 27 | #else 28 | [ bonds ] 29 | ; i j funct length force.c. 30 | 1 2 1 0.1 463700 ; orig was 0.1 345000, see mailing lists 31 | 1 3 1 0.1 463700 ; orig was 0.1 345000, see mailing lists 32 | 33 | [ angles ] 34 | ; i j k funct angle force.c. 35 | 2 1 3 1 109.47 383 109.47 383 36 | #endif 37 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # ClayFF: 2 | # A GROMACS implementation of the ClayFF force field 3 | 4 | ## An old tutorial... 5 | 6 | [GROMACS LINK:] 7 | 8 | 9 | 10 | [MDP OPTIONS (aka simulation settings):] 11 | 12 | 13 | 14 | [SUPER GOOD TUTORIALS (albeit, not mineral related):] 15 | 16 | 17 | 18 | [BRIEF WORKTHROUGH OF USING GROMACS:] 19 | 20 | 1. ***Files needed:*** 21 | 22 | a. A set of FF parameters (.ff Folder) -- Lots built into gromacs, 23 | but mainly bio related. See attachment for an example of ClayFF. 24 | 25 | b. Structure file (.pdb/.gro). 26 | 27 | c. Topology file (.top) -- links the structure file to FF folder. 28 | 29 | d. Simulation settings input file (.mdp). 30 | 31 | e. Jobscript. 32 | 33 | 2. ***Installing gromacs on Ubuntu:*** 34 | 35 | Installing gromacs on Ubuntu should be fairly simple. Firstly, you 36 | should update Ubuntu's package-manager (apt-get). You can think of 37 | apt-get as a command-line driven app-store. 38 | 39 | Run the commands: 40 | ```shell 41 | sudo apt-get update 42 | sudo apt-get upgrade 43 | ``` 44 | 45 | This should update the package-manager and then upgrade all default 46 | installed packages in Ubuntu. 47 | 48 | If you want to see what version of gromacs will be installed, as well as 49 | all the requisite softwares that will be installed alongside gromacs, 50 | run: 51 | ```shell 52 | apt-cache show gromacs 53 | ``` 54 | Finally, to install gromacs you can run: 55 | ```shell 56 | sudo apt-get install gromacs 57 | ``` 58 | N.B. be careful using the sudo command as it grants unlimited power! 59 | It's very easy to break a machine by typing the wrong command into the 60 | terminal with sudo. 61 | 62 | Let's also install some other useful software from the command line. 63 | ```shell 64 | sudo apt-get install grace 65 | sudo apt-get install gnuplot 66 | ``` 67 | Grace is the default plotting tool used in conjunction with gromacs. I 68 | personally prefer gnuplot, so I tend to install both. 69 | 70 | You will need to install VMD by hand, as it has unusual licensing 71 | issues. 72 | 73 | Feel free to install any further software you like. 74 | 75 | 3. ***Example Simulation:*** 76 | 77 | Within the attached archive you should find all the files required to 78 | run a simple simulation of pyrophyllite (an uncharged clay mineral) with 79 | water. 80 | 81 | The files should contain the following... 82 | 83 | ![](./media/image1.png) 84 | 85 | One quirk of gromacs is that we need to run separate simulations for 86 | energy minimization, equilibration and production. 87 | 88 | This can be scripted once you are comfortable with the overall workflow, 89 | but I still break my simulations down into smaller chunks in case 90 | something goes wrong. 91 | 92 | I tend to setup my simulation in the 00_setup folder and run all the 93 | simulations in the subsequent folders. 94 | 95 | Feel free to explore the files to try and understand how each file links 96 | to one another. 97 | 98 | First, open up a terminal in the 00_setup folder. 99 | 100 | The PyroUnitCell.gro file is the unitcell of our mineral. We are 101 | fortunate that ClayFF is almost entirely nonbonded. In this sense, we 102 | can treat our unit cell like a single molecule and repeat it in xyz to 103 | create a slab, without having to worry about bonds, angles and dihedrals 104 | between adjacent unit cells. 105 | 106 | This won't be the case with interface, so we'll need to think about how 107 | to make the initial structures a bit better. 108 | 109 | If you run the following command, you shall replicate the unit cell in 110 | xyz to generate a slab structure. 111 | ```shell 112 | gmx genconf --f PyroUnitCell.gro --nbox 6 4 2 --o slab.gro 113 | ``` 114 | You should now have a structure called slab.gro that is 6x4x2 unit 115 | cells. 116 | 117 | ![](./media/image2.png) 118 | 119 | N.B. You can use the --h flag at the end of any gromacs command to find 120 | more information about how the command works, its inputs and outputs, 121 | etc... For example: 122 | ```shell 123 | gmx genconf -h 124 | ``` 125 | You'll now need to amend the topology slightly to fix for the fact that 126 | we have 48 unit cells in our structure, rather than just 1. 127 | 128 | Open up the topol.top file and change the number 1 on the last line to 129 | 48. 130 | 131 | Now let's add some water to the system. 132 | 133 | Open up the slab.gro file and scroll down to the bottom. 134 | 135 | The last three numbers are the {x,y,z} size of the overall simulation 136 | structure. Edit the last number (z) to include some vacuum space. 137 | 138 | For example, the last three numbers of my slab.gro file are now... 139 | ``` 140 | 3.09600 3.58640 3.0000 141 | ``` 142 | Now run the command: 143 | ```shell 144 | gmx solvate -cp slab.gro -cs spc216.gro -p topol.top -o solvated.gro 145 | ``` 146 | This will add SPC water molecules into the system. The spc216.gro file 147 | is hidden in gromacs default libraries, there are other default solvents 148 | you can use, but I forget what they are at the moment! 149 | 150 | Note now that the topol.top file contains water molecules. In my case 151 | 391 water molecules. 152 | 153 | ![](./media/image3.png) 154 | 155 | Change directory to the 01_min folder and run the following command: 156 | ```shell 157 | gmx grompp -f energy_min.mdp -c ../00_setup/solvated.gro -p ../00_setup/topol.top -maxwarn 1 158 | ``` 159 | Note that I had a slight mismatch in whitespace between atom naming's in 160 | the structure file and the topology. This meant that I had to use the 161 | --maxwarn 1 flag to ignore this warning. Always be sure to check what 162 | the warnings mean before ignoring them, gromacs won't let you proceed 163 | with un-ignored warnings. 164 | 165 | The grompp command should have 'compiled' a binary .tpr file. This .tpr 166 | file is the input to your simulation. The .tpr file contains all the 167 | information about the system you wish to run. It is portable, so I 168 | typically make my .tpr files on my local machine and then run the 169 | simulation on a cluster. 170 | 171 | To run the energy minimization, run the command: 172 | ```shell 173 | gmx mdrun -s topol.tpr --v 174 | ``` 175 | gromacs should produce several files during the simulation. 176 | 177 | The confout.gro file is the final structure of the energy minimization 178 | process. This is the file that you should feed into equilibration MD. 179 | 180 | The ener.edr is a binary file that contains all the information 181 | regarding the energies of the system. This can be analysed using the gmx 182 | energy command (see later). 183 | 184 | The traj.trr file is the trajectory calculated by gromacs throughout the 185 | simulation. 186 | 187 | Next, change folder to the 02_eqm folder and run the following command. 188 | ```shell 189 | gmx grompp -f equil_md.mdp -c ../01_min/confout.gro -p ../00_setup/topol.top 190 | ``` 191 | This shall now setup the equilibration MD run from our energy minimized 192 | structure. 193 | 194 | Again, run the following command to start the simulation: 195 | ```shell 196 | gmx mdrun -s topol.tpr --v 197 | ``` 198 | Now that the simulation is complete, let us analyse some of the output 199 | data: 200 | 201 | The energies of the system can be analysed using the command: 202 | ```shell 203 | gmx energy --f ener.edr 204 | ``` 205 | The 1d-density profiles of the system can be analysed using the command: 206 | ```shell 207 | gmx density -f traj.trr 208 | ``` 209 | There is a tonne of other inbuilt analysis tools. To see them all, type: 210 | ```shell 211 | gmx help commands 212 | ``` 213 | From here you would need to check for true equilibration before running 214 | a production simulation. The process is exactly the same as running the 215 | equilibration MD, but some of the setting in the input .mdp file are 216 | slightly different. 217 | 218 | I would now recommend exploring the .mdp files, seeing what each command 219 | does. Also explore the potential options in the second link on the first 220 | page. Finally, work through some of Justin's tutorials for a more 221 | indepth understanding of how gromacs works from a bio points of view. 222 | 223 | ![](./media/image4.png) 224 | 225 | Plot of total energy against time \^ 226 | 227 | ![](./media/image5.png) 228 | 229 | Density profile of water molecule in the system \^ 230 | -------------------------------------------------------------------------------- /examples/montmorrilonite/MontARUC.gro: -------------------------------------------------------------------------------- 1 | Montmorillonite Unit Cell 2 | 40 3 | 1MON HO1 1 0.084 0.120 0.595 4 | 1MON HO2 2 0.181 0.230 0.205 5 | 1MON HO3 3 0.441 0.679 0.205 6 | 1MON HO4 4 0.344 0.568 0.595 7 | 1MON OHS1 5 0.101 0.122 0.499 8 | 1MON OHS2 6 0.163 0.228 0.301 9 | 1MON OH1 7 0.424 0.677 0.301 10 | 1MON OH2 8 0.362 0.570 0.499 11 | 1MON OBS1 9 0.317 0.847 0.506 12 | 1MON OBS2 10 0.361 0.225 0.507 13 | 1MON OB1 11 0.463 0.400 0.294 14 | 1MON OBS3 12 0.419 0.125 0.294 15 | 1MON OBS4 13 0.202 0.848 0.294 16 | 1MON OB2 14 0.164 0.574 0.294 17 | 1MON OB3 15 0.062 0.399 0.506 18 | 1MON OB4 16 0.106 0.673 0.507 19 | 1MON OB5 17 0.485 0.293 0.730 20 | 1MON OB6 18 0.316 0.091 0.729 21 | 1MON OB7 19 0.229 0.342 0.706 22 | 1MON OB8 20 0.295 0.057 0.070 23 | 1MON OB9 21 0.464 0.259 0.071 24 | 1MON OB10 22 0.035 0.008 0.095 25 | 1MON OB11 23 0.040 0.505 0.070 26 | 1MON OB12 24 0.209 0.707 0.071 27 | 1MON OB13 25 0.296 0.457 0.095 28 | 1MON OB14 26 0.229 0.742 0.730 29 | 1MON OB15 27 0.061 0.539 0.729 30 | 1MON OB16 28 0.490 0.790 0.706 31 | 1MON MGO1 29 0.260 0.101 0.400 32 | 1MON AO1 30 0.004 0.249 0.400 33 | 1MON AO2 31 0.265 0.698 0.400 34 | 1MON AO3 32 0.005 0.549 0.400 35 | 1MON ST1 33 0.336 0.840 0.668 36 | 1MON ST2 34 0.346 0.238 0.669 37 | 1MON ST3 35 0.444 0.407 0.132 38 | 1MON ST4 36 0.434 0.112 0.131 39 | 1MON ST5 37 0.183 0.856 0.132 40 | 1MON ST6 38 0.179 0.561 0.131 41 | 1MON ST7 39 0.081 0.391 0.668 42 | 1MON ST8 40 0.091 0.686 0.669 43 | ; 1MON NA1 41 0.170 0.239 0.867 44 | 0.5160 0.8966 0.9347 45 | -------------------------------------------------------------------------------- /examples/montmorrilonite/ffMontAR.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; 3 | [ moleculetype ] 4 | ; name nrexcl 5 | MON 1 6 | 7 | [ atoms ] 8 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 9 | ; residue 1 MON rtp MON q 0.0 10 | 1 ho 1 MON HO1 1 0.425 1.008 ; qtot 0.425 11 | 2 ho 1 MON HO2 2 0.425 1.008 ; qtot 0.85 12 | 3 ho 1 MON HO3 3 0.425 1.008 ; qtot 1.275 13 | 4 ho 1 MON HO4 4 0.425 1.008 ; qtot 1.7 14 | 5 ohs 1 MON OHS1 5 -1.0808 16 ; qtot 0.6192 15 | 6 ohs 1 MON OHS2 6 -1.0808 16 ; qtot -0.4616 16 | 7 oh 1 MON OH1 7 -0.95 16 ; qtot -1.412 17 | 8 oh 1 MON OH2 8 -0.95 16 ; qtot -2.362 18 | 9 obos 1 MON OBS1 9 -1.1808 16 ; qtot -3.542 19 | 10 obos 1 MON OBS2 10 -1.1808 16 ; qtot -4.723 20 | 11 ob 1 MON OB1 11 -1.05 16 ; qtot -5.773 21 | 12 obos 1 MON OBS3 12 -1.1808 16 ; qtot -6.954 22 | 13 obos 1 MON OBS4 13 -1.1808 16 ; qtot -8.135 23 | 14 ob 1 MON OB2 14 -1.05 16 ; qtot -9.185 24 | 15 ob 1 MON OB3 15 -1.05 16 ; qtot -10.23 25 | 16 ob 1 MON OB4 16 -1.05 16 ; qtot -11.28 26 | 17 ob 1 MON OB5 17 -1.05 16 ; qtot -12.33 27 | 18 ob 1 MON OB6 18 -1.05 16 ; qtot -13.38 28 | 19 ob 1 MON OB7 19 -1.05 16 ; qtot -14.43 29 | 20 ob 1 MON OB8 20 -1.05 16 ; qtot -15.48 30 | 21 ob 1 MON OB9 21 -1.05 16 ; qtot -16.53 31 | 22 ob 1 MON OB10 22 -1.05 16 ; qtot -17.58 32 | 23 ob 1 MON OB11 23 -1.05 16 ; qtot -18.63 33 | 24 ob 1 MON OB12 24 -1.05 16 ; qtot -19.68 34 | 25 ob 1 MON OB13 25 -1.05 16 ; qtot -20.73 35 | 26 ob 1 MON OB14 26 -1.05 16 ; qtot -21.78 36 | 27 ob 1 MON OB15 27 -1.05 16 ; qtot -22.83 37 | 28 ob 1 MON OB16 28 -1.05 16 ; qtot -23.88 38 | 29 mgo 1 MON MGO1 29 1.3598 24.31 ; qtot -22.52 39 | 30 ao 1 MON AO1 30 1.575 26.98 ; qtot -20.95 40 | 31 ao 1 MON AO2 31 1.575 26.98 ; qtot -19.37 41 | 32 ao 1 MON AO3 32 1.575 26.98 ; qtot -17.8 42 | 33 st 1 MON ST1 33 2.1 28.09 ; qtot -15.7 43 | 34 st 1 MON ST2 34 2.1 28.09 ; qtot -13.6 44 | 35 st 1 MON ST3 35 2.1 28.09 ; qtot -11.5 45 | 36 st 1 MON ST4 36 2.1 28.09 ; qtot -9.4 46 | 37 st 1 MON ST5 37 2.1 28.09 ; qtot -7.3 47 | 38 st 1 MON ST6 38 2.1 28.09 ; qtot -5.2 48 | 39 st 1 MON ST7 39 2.1 28.09 ; qtot -3.1 49 | 40 st 1 MON ST8 40 2.1 28.09 ; qtot -1 50 | ; 41 Na 1 MON NA1 41 1 22.99 ; qtot 0 51 | 52 | 53 | [ bonds ] 54 | ; i j funct length force.c. 55 | 1 5 1 0.1 463532.808 56 | 2 6 1 0.1 463532.808 57 | 3 7 1 0.1 463532.808 58 | 4 8 1 0.1 463532.808 59 | -------------------------------------------------------------------------------- /examples/montmorrilonite/topol.top: -------------------------------------------------------------------------------- 1 | ; include params for ClayFF 2 | #include "./ClayFF.ff/forcefield.itp" 3 | 4 | ; Include the individual topology for clay 5 | #include "./ffMontAR.itp" 6 | 7 | ; Include the individual topology for SPC water 8 | #include "./ClayFF.ff/spce.itp" 9 | #include "./ClayFF.ff/ions.itp" 10 | 11 | [ system ] 12 | ; Name 13 | MMT in water 14 | 15 | [ molecules ] 16 | ; Compound #mols 17 | MON 1 -------------------------------------------------------------------------------- /examples/pyrophyllite/PyroUnitCell.gro: -------------------------------------------------------------------------------- 1 | Pyrophyllite Unit Cell 2 | 40 3 | 1PYRO HO1 1 0.084 0.120 0.595 4 | 1PYRO HO2 2 0.181 0.230 0.205 5 | 1PYRO HO3 3 0.441 0.679 0.205 6 | 1PYRO HO4 4 0.344 0.568 0.595 7 | 1PYRO OH1 5 0.101 0.122 0.499 8 | 1PYRO OH2 6 0.163 0.228 0.301 9 | 1PYRO OH3 7 0.424 0.677 0.301 10 | 1PYRO OH4 8 0.362 0.570 0.499 11 | 1PYRO OB1 9 0.317 0.847 0.506 12 | 1PYRO OB2 10 0.361 0.225 0.507 13 | 1PYRO OB3 11 0.463 0.400 0.294 14 | 1PYRO OB4 12 0.419 0.125 0.294 15 | 1PYRO OB5 13 0.202 0.848 0.294 16 | 1PYRO OB6 14 0.164 0.574 0.294 17 | 1PYRO OB7 15 0.062 0.399 0.506 18 | 1PYRO OB8 16 0.106 0.673 0.507 19 | 1PYRO OB9 17 0.485 0.293 0.730 20 | 1PYRO OB10 18 0.316 0.091 0.729 21 | 1PYRO OB11 19 0.229 0.342 0.706 22 | 1PYRO OB12 20 0.295 0.057 0.070 23 | 1PYRO OB13 21 0.464 0.259 0.071 24 | 1PYRO OB14 22 0.035 0.008 0.095 25 | 1PYRO OB15 23 0.040 0.505 0.070 26 | 1PYRO OB16 24 0.209 0.707 0.071 27 | 1PYRO OB17 25 0.296 0.457 0.095 28 | 1PYRO OB18 26 0.229 0.742 0.730 29 | 1PYRO OB19 27 0.061 0.539 0.729 30 | 1PYRO OB20 28 0.490 0.790 0.706 31 | 1PYRO AO1 29 0.260 0.101 0.400 32 | 1PYRO AO2 30 0.004 0.249 0.400 33 | 1PYRO AO3 31 0.265 0.698 0.400 34 | 1PYRO AO4 32 0.005 0.549 0.400 35 | 1PYRO ST1 33 0.336 0.840 0.668 36 | 1PYRO ST2 34 0.346 0.238 0.669 37 | 1PYRO ST3 35 0.444 0.407 0.132 38 | 1PYRO ST4 36 0.434 0.112 0.131 39 | 1PYRO ST5 37 0.183 0.856 0.132 40 | 1PYRO ST6 38 0.179 0.561 0.131 41 | 1PYRO ST7 39 0.081 0.391 0.668 42 | 1PYRO ST8 40 0.091 0.686 0.669 43 | 0.5160 0.8966 0.9347 44 | -------------------------------------------------------------------------------- /examples/pyrophyllite/ffPyroUC.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; 3 | [ moleculetype ] 4 | ; name nrexcl 5 | PYR 1 6 | 7 | [ atoms ] 8 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 9 | ; residue 1 PYR rtp PYR q 0.0 10 | 1 ho 1 PYR HO1 1 0.425 1.008 11 | 2 ho 1 PYR HO2 2 0.425 1.008 12 | 3 ho 1 PYR HO3 3 0.425 1.008 13 | 4 ho 1 PYR HO4 4 0.425 1.008 14 | 5 oh 1 PYR OH1 5 -0.95 16 15 | 6 oh 1 PYR OH2 6 -0.95 16 16 | 7 oh 1 PYR OH3 7 -0.95 16 17 | 8 oh 1 PYR OH4 8 -0.95 16 18 | 9 ob 1 PYR OB1 9 -1.05 16 19 | 10 ob 1 PYR OB2 10 -1.05 16 20 | 11 ob 1 PYR OB3 11 -1.05 16 21 | 12 ob 1 PYR OB4 12 -1.05 16 22 | 13 ob 1 PYR OB5 13 -1.05 16 23 | 14 ob 1 PYR OB6 14 -1.05 16 24 | 15 ob 1 PYR OB7 15 -1.05 16 25 | 16 ob 1 PYR OB8 16 -1.05 16 26 | 17 ob 1 PYR OB9 17 -1.05 16 27 | 18 ob 1 PYR OB10 18 -1.05 16 28 | 19 ob 1 PYR OB11 19 -1.05 16 29 | 20 ob 1 PYR OB12 20 -1.05 16 30 | 21 ob 1 PYR OB13 21 -1.05 16 31 | 22 ob 1 PYR OB14 22 -1.05 16 32 | 23 ob 1 PYR OB15 23 -1.05 16 33 | 24 ob 1 PYR OB16 24 -1.05 16 34 | 25 ob 1 PYR OB17 25 -1.05 16 35 | 26 ob 1 PYR OB18 26 -1.05 16 36 | 27 ob 1 PYR OB19 27 -1.05 16 37 | 28 ob 1 PYR OB20 28 -1.05 16 38 | 29 ao 1 PYR AO1 29 1.575 26.98 39 | 30 ao 1 PYR AO2 30 1.575 26.98 40 | 31 ao 1 PYR AO3 31 1.575 26.98 41 | 32 ao 1 PYR AO4 32 1.575 26.98 42 | 33 st 1 PYR ST1 33 2.1 28.09 43 | 34 st 1 PYR ST2 34 2.1 28.09 44 | 35 st 1 PYR ST3 35 2.1 28.09 45 | 36 st 1 PYR ST4 36 2.1 28.09 46 | 37 st 1 PYR ST5 37 2.1 28.09 47 | 38 st 1 PYR ST6 38 2.1 28.09 48 | 39 st 1 PYR ST7 39 2.1 28.09 49 | 40 st 1 PYR ST8 40 2.1 28.09 50 | 51 | [ bonds ] 52 | ; i j funct length force.c. 53 | 1 5 1 0.1 463532.808 54 | 2 6 1 0.1 463532.808 55 | 3 7 1 0.1 463532.808 56 | 4 8 1 0.1 463532.808 57 | -------------------------------------------------------------------------------- /examples/pyrophyllite/topol.top: -------------------------------------------------------------------------------- 1 | ; include params for ClayFF 2 | #include "./ClayFF.ff/forcefield.itp" 3 | 4 | ; Include the individual topology for clay 5 | #include "./ffPyroUC.itp" 6 | 7 | ; Include the individual topology for SPC water 8 | #include "./ClayFF.ff/spc.itp" 9 | 10 | [ system ] 11 | ; Name 12 | Pyrophyllite in water 13 | 14 | [ molecules ] 15 | ; Compound #mols 16 | PYR 1 17 | -------------------------------------------------------------------------------- /media/image1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomasunderwood/ClayFF/137ea3256db2a3c66f90f834084772aa406e90ad/media/image1.png -------------------------------------------------------------------------------- /media/image2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomasunderwood/ClayFF/137ea3256db2a3c66f90f834084772aa406e90ad/media/image2.png -------------------------------------------------------------------------------- /media/image3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomasunderwood/ClayFF/137ea3256db2a3c66f90f834084772aa406e90ad/media/image3.png -------------------------------------------------------------------------------- /media/image4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomasunderwood/ClayFF/137ea3256db2a3c66f90f834084772aa406e90ad/media/image4.png -------------------------------------------------------------------------------- /media/image5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomasunderwood/ClayFF/137ea3256db2a3c66f90f834084772aa406e90ad/media/image5.png -------------------------------------------------------------------------------- /tutorial/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomasunderwood/ClayFF/137ea3256db2a3c66f90f834084772aa406e90ad/tutorial/.DS_Store -------------------------------------------------------------------------------- /tutorial/GROMACS_tutorial.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomasunderwood/ClayFF/137ea3256db2a3c66f90f834084772aa406e90ad/tutorial/GROMACS_tutorial.docx -------------------------------------------------------------------------------- /tutorial/clayFF_example/00_setup/ClayFF.ff/atomtypes.atp: -------------------------------------------------------------------------------- 1 | hw 1.008 ; water hydrogen 2 | ho 1.008 ; hydroxyl hydrogen 3 | ow 16.00 ; water hydrogen 4 | oh 16.00 ; hydroxyl oxygen 5 | ob 16.00 ; bridging oxygen 6 | obos 16.00 ; bridging oxygen with octahedral substitution 7 | obts 16.00 ; bridging oxygen with tetrahedral substitution 8 | obss 16.00 ; bridging oxygen with double substitution 9 | ohs 16.00 ; hydroxyl oxygen with substitution 10 | st 28.09 ; tetrahedral silicon 11 | ao 26.98 ; octahedral aluminum 12 | at 26.98 ; tetrahedral aluminum 13 | mgo 24.31 ; octahedral magnesium 14 | mgh 24.31 ; hydroxide magnesium 15 | cao 40.08 ; octahedral calcium 16 | cah 40.08 ; hydroxide calcium 17 | feo 55.85 ; octahedral iron 18 | lio 6.941 ; octahedral lithium 19 | Na 22.99 ; aqueous sodium ion 20 | K 39.10 ; aqueous potassium ion 21 | Cs 132.9 ; aqueous cesium ion 22 | Ca 40.08 ; aqueous calcium ion 23 | Ba 137.3 ; aqueous barium ion 24 | Cl 35.45 ; aqueous chloride ion 25 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/00_setup/ClayFF.ff/ffbonded.itp: -------------------------------------------------------------------------------- 1 | ; Bond type code 2 | ; when converting from ClayFF to Gromacs use 1cal - 4.186 J 3 | ; also need to multiply k by 2 4 | ; 5 | #define oh 0.1 463532.8 6 | ; hydroxil bond 7 | ; 8 | #define ohs 0.1 463532.8 9 | ; hydroxil bond with substitution 10 | ; 11 | #define ohw 0.1 463532.8 12 | ; water bond 13 | ; 14 | ; 15 | ;for konversion use 1 kcal/mol A^2 = 418.6 kJ/mol nm^2 16 | ;also multiply by 2 17 | ; 18 | ; Bond-angle type code 19 | ; 20 | #define hoh 109.47 383.0 21 | ; water angle 22 | ; 23 | #define moh 109.47 251.2 24 | ; metal-oh 25 | ; 26 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/00_setup/ClayFF.ff/ffnonbonded.itp: -------------------------------------------------------------------------------- 1 | [ atomtypes ] 2 | ; atom descriptions and masses are assigned in ffclayff.atp 3 | ; name at.number mass charge ptype sigma epsilon 4 | hw 1 1.008 0.4100 A 0.0 0.0 5 | ho 1 1.008 0.4250 A 0.0 0.0 6 | ow 8 16.000 -0.8200 A 3.1655E-01 6.502E-01 7 | oh 8 16.000 -0.9500 A 3.1655E-01 6.502E-01 8 | ob 8 16.000 -1.0500 A 3.1655E-01 6.502E-01 9 | obos 8 16.000 -1.1808 A 3.1655E-01 6.502E-01 10 | obts 8 16.000 -1.1688 A 3.1655E-01 6.502E-01 11 | obss 8 16.000 -1.2996 A 3.1655E-01 6.502E-01 12 | ohs 8 16.000 -1.0808 A 3.1655E-01 6.502E-01 13 | st 16 28.090 2.1000 A 3.3020E-01 7.701E-06 14 | ao 13 26.980 1.5750 A 4.2712E-01 5.564E-06 15 | at 13 26.980 1.5750 A 3.3020E-01 7.701E-06 16 | mgo 12 24.310 1.3600 A 5.2643E-01 3.778E-06 17 | mgh 12 24.310 1.0500 A 5.2643E-01 3.778E-06 18 | cao 20 40.080 1.3600 A 5.5667E-01 2.104E-05 19 | cah 20 40.080 1.0500 A 5.5617E-01 2.104E-05 20 | feo 26 55.850 1.5750 A 4.9062E-01 3.778E-05 21 | lio 3 6.941 0.5250 A 4.2101E-01 3.778E-05 22 | Na 11 22.990 1.0000 A 2.3500E-01 5.4392E-01 23 | k 19 39.100 1.0000 A 3.3340E-01 4.184E-01 24 | Cs 55 132.900 1.0000 A 3.8310E-01 4.184E-01 25 | Ca 20 40.080 2.0000 A 2.8720E-01 4.184E-01 26 | Ba 56 137.300 2.0000 A 3.8166E-01 1.966E-01 27 | Cl 17 34.450 -1.0000 A 4.4000E-01 4.184E-01 28 | 29 | HW 1 1.008 0.4100 A 0.0 0.0 30 | HO 1 1.008 0.4250 A 0.0 0.0 31 | OW 8 16.000 -0.8200 A 3.1655E-01 6.502E-01 32 | OH 8 16.000 -0.9500 A 3.1655E-01 6.502E-01 33 | OB 8 16.000 -1.0500 A 3.1655E-01 6.502E-01 34 | OBOS 8 16.000 -1.1808 A 3.1655E-01 6.502E-01 35 | OBTS 8 16.000 -1.1688 A 3.1655E-01 6.502E-01 36 | OBSS 8 16.000 -1.2996 A 3.1655E-01 6.502E-01 37 | OHS 8 16.000 -1.0808 A 3.1655E-01 6.502E-01 38 | ST 16 28.090 2.1000 A 3.3020E-01 7.701E-06 39 | AO 13 26.980 1.5750 A 4.2712E-01 5.564E-06 40 | AT 13 26.980 1.5750 A 3.3020E-01 7.701E-06 41 | MGO 12 24.310 1.3600 A 5.2643E-01 3.778E-06 42 | MGH 12 24.310 1.0500 A 5.2643E-01 3.778E-06 43 | CAO 20 40.080 1.3600 A 5.5667E-01 2.104E-05 44 | CAH 20 40.080 1.0500 A 5.5617E-01 2.104E-05 45 | FEO 26 55.850 1.5750 A 4.9062E-01 3.778E-05 46 | LIO 3 6.941 0.5250 A 4.2101E-01 3.778E-05 47 | NA 11 22.990 1.0000 A 2.3500E-01 5.4392E-01 48 | K 19 39.100 1.0000 A 3.3340E-01 4.184E-01 49 | CS 55 132.900 1.0000 A 3.8310E-01 4.184E-01 50 | CA 20 40.080 2.0000 A 2.8720E-01 4.184E-01 51 | BA 56 137.300 2.0000 A 3.8166E-01 1.966E-01 52 | CL 17 34.450 -1.0000 A 4.4000E-01 4.184E-01 53 | 54 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/00_setup/ClayFF.ff/forcefield.doc: -------------------------------------------------------------------------------- 1 | ClayFF v.1 2 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/00_setup/ClayFF.ff/forcefield.itp: -------------------------------------------------------------------------------- 1 | #define _ClayFF_TOM 2 | 3 | [ defaults ] 4 | ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 5 | 1 2 yes 1.0 1.0 6 | 7 | #include "./ffnonbonded.itp" 8 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/00_setup/ClayFF.ff/ions.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | NA 1 4 | 5 | [ atoms ] 6 | ; id at type res nr residu name at name cg nr charge 7 | 1 NA 1 NA NA 1 1 8 | 9 | [ moleculetype ] 10 | ; molname nrexcl 11 | K 1 12 | 13 | [ atoms ] 14 | ; id at type res nr residu name at name cg nr charge 15 | 1 K 1 K K 1 1 16 | 17 | [ moleculetype ] 18 | ; molname nrexcl 19 | CS 1 20 | 21 | [ atoms ] 22 | ; id at type res nr residu name at name cg nr charge 23 | 1 CS 1 CS CS 1 1 24 | 25 | [ moleculetype ] 26 | ; molname nrexcl 27 | CA 1 28 | 29 | [ atoms ] 30 | ; id at type res nr residu name at name cg nr charge 31 | 1 CA 1 CA CA 1 2 32 | 33 | [ moleculetype ] 34 | ; molname nrexcl 35 | BA 1 36 | 37 | [ atoms ] 38 | ; id at type res nr residu name at name cg nr charge 39 | 1 BA 1 BA BA 1 2 40 | 41 | [ moleculetype ] 42 | ; molname nrexcl 43 | CL 1 44 | 45 | [ atoms ] 46 | ; id at type res nr residu name at name cg nr charge 47 | 1 CL 1 CL CL 1 -1 48 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/00_setup/ClayFF.ff/spc.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | SOL 2 4 | 5 | [ atoms ] 6 | ; nr type resnr residue atom cgnr charge mass 7 | 1 OW 1 SOL OW 1 -0.82 8 | 2 HW 1 SOL HW1 1 0.41 9 | 3 HW 1 SOL HW2 1 0.41 10 | 11 | #ifndef FLEXIBLE 12 | [ settles ] 13 | ; OW funct doh dhh 14 | 1 1 0.1 0.16330 15 | 16 | [ exclusions ] 17 | 1 2 3 18 | 2 1 3 19 | 3 1 2 20 | #else 21 | [ bonds ] 22 | ; i j funct length force.c. 23 | 1 2 1 0.1 345000 0.1 345000 24 | 1 3 1 0.1 345000 0.1 345000 25 | 26 | [ angles ] 27 | ; i j k funct angle force.c. 28 | 2 1 3 1 109.47 383 109.47 383 29 | #endif 30 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/00_setup/PyroUnitCell.gro: -------------------------------------------------------------------------------- 1 | Pyrophyllite Unit Cell 2 | 40 3 | 1PYRO HO1 1 0.084 0.120 0.595 4 | 1PYRO HO2 2 0.181 0.230 0.205 5 | 1PYRO HO3 3 0.441 0.679 0.205 6 | 1PYRO HO4 4 0.344 0.568 0.595 7 | 1PYRO OH1 5 0.101 0.122 0.499 8 | 1PYRO OH2 6 0.163 0.228 0.301 9 | 1PYRO OH3 7 0.424 0.677 0.301 10 | 1PYRO OH4 8 0.362 0.570 0.499 11 | 1PYRO OB1 9 0.317 0.847 0.506 12 | 1PYRO OB2 10 0.361 0.225 0.507 13 | 1PYRO OB3 11 0.463 0.400 0.294 14 | 1PYRO OB4 12 0.419 0.125 0.294 15 | 1PYRO OB5 13 0.202 0.848 0.294 16 | 1PYRO OB6 14 0.164 0.574 0.294 17 | 1PYRO OB7 15 0.062 0.399 0.506 18 | 1PYRO OB8 16 0.106 0.673 0.507 19 | 1PYRO OB9 17 0.485 0.293 0.730 20 | 1PYRO OB10 18 0.316 0.091 0.729 21 | 1PYRO OB11 19 0.229 0.342 0.706 22 | 1PYRO OB12 20 0.295 0.057 0.070 23 | 1PYRO OB13 21 0.464 0.259 0.071 24 | 1PYRO OB14 22 0.035 0.008 0.095 25 | 1PYRO OB15 23 0.040 0.505 0.070 26 | 1PYRO OB16 24 0.209 0.707 0.071 27 | 1PYRO OB17 25 0.296 0.457 0.095 28 | 1PYRO OB18 26 0.229 0.742 0.730 29 | 1PYRO OB19 27 0.061 0.539 0.729 30 | 1PYRO OB20 28 0.490 0.790 0.706 31 | 1PYRO AO1 29 0.260 0.101 0.400 32 | 1PYRO AO2 30 0.004 0.249 0.400 33 | 1PYRO AO3 31 0.265 0.698 0.400 34 | 1PYRO AO4 32 0.005 0.549 0.400 35 | 1PYRO ST1 33 0.336 0.840 0.668 36 | 1PYRO ST2 34 0.346 0.238 0.669 37 | 1PYRO ST3 35 0.444 0.407 0.132 38 | 1PYRO ST4 36 0.434 0.112 0.131 39 | 1PYRO ST5 37 0.183 0.856 0.132 40 | 1PYRO ST6 38 0.179 0.561 0.131 41 | 1PYRO ST7 39 0.081 0.391 0.668 42 | 1PYRO ST8 40 0.091 0.686 0.669 43 | 0.5160 0.8966 0.9347 44 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/00_setup/ffPyroUC.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; 3 | [ moleculetype ] 4 | ; name nrexcl 5 | PYR 1 6 | 7 | [ atoms ] 8 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 9 | ; residue 1 PYR rtp PYR q 0.0 10 | 1 ho 1 PYR HO1 1 0.425 1.008 11 | 2 ho 1 PYR HO2 2 0.425 1.008 12 | 3 ho 1 PYR HO3 3 0.425 1.008 13 | 4 ho 1 PYR HO4 4 0.425 1.008 14 | 5 oh 1 PYR OH1 5 -0.95 16 15 | 6 oh 1 PYR OH2 6 -0.95 16 16 | 7 oh 1 PYR OH3 7 -0.95 16 17 | 8 oh 1 PYR OH4 8 -0.95 16 18 | 9 ob 1 PYR OB1 9 -1.05 16 19 | 10 ob 1 PYR OB2 10 -1.05 16 20 | 11 ob 1 PYR OB3 11 -1.05 16 21 | 12 ob 1 PYR OB4 12 -1.05 16 22 | 13 ob 1 PYR OB5 13 -1.05 16 23 | 14 ob 1 PYR OB6 14 -1.05 16 24 | 15 ob 1 PYR OB7 15 -1.05 16 25 | 16 ob 1 PYR OB8 16 -1.05 16 26 | 17 ob 1 PYR OB9 17 -1.05 16 27 | 18 ob 1 PYR OB10 18 -1.05 16 28 | 19 ob 1 PYR OB11 19 -1.05 16 29 | 20 ob 1 PYR OB12 20 -1.05 16 30 | 21 ob 1 PYR OB13 21 -1.05 16 31 | 22 ob 1 PYR OB14 22 -1.05 16 32 | 23 ob 1 PYR OB15 23 -1.05 16 33 | 24 ob 1 PYR OB16 24 -1.05 16 34 | 25 ob 1 PYR OB17 25 -1.05 16 35 | 26 ob 1 PYR OB18 26 -1.05 16 36 | 27 ob 1 PYR OB19 27 -1.05 16 37 | 28 ob 1 PYR OB20 28 -1.05 16 38 | 29 ao 1 PYR AO1 29 1.575 26.98 39 | 30 ao 1 PYR AO2 30 1.575 26.98 40 | 31 ao 1 PYR AO3 31 1.575 26.98 41 | 32 ao 1 PYR AO4 32 1.575 26.98 42 | 33 st 1 PYR ST1 33 2.1 28.09 43 | 34 st 1 PYR ST2 34 2.1 28.09 44 | 35 st 1 PYR ST3 35 2.1 28.09 45 | 36 st 1 PYR ST4 36 2.1 28.09 46 | 37 st 1 PYR ST5 37 2.1 28.09 47 | 38 st 1 PYR ST6 38 2.1 28.09 48 | 39 st 1 PYR ST7 39 2.1 28.09 49 | 40 st 1 PYR ST8 40 2.1 28.09 50 | 51 | [ bonds ] 52 | ; i j funct length force.c. 53 | 1 5 1 0.1 463532.808 54 | 2 6 1 0.1 463532.808 55 | 3 7 1 0.1 463532.808 56 | 4 8 1 0.1 463532.808 57 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/00_setup/topol.top: -------------------------------------------------------------------------------- 1 | ; include params for ClayFF 2 | #include "./ClayFF.ff/forcefield.itp" 3 | 4 | ; Include the individual topology for clay 5 | #include "./ffPyroUC.itp" 6 | 7 | ; Include the individual topology for SPC water 8 | #include "./ClayFF.ff/spc.itp" 9 | 10 | [ system ] 11 | ; Name 12 | Pyrophyllite in water 13 | 14 | [ molecules ] 15 | ; Compound #mols 16 | PYR 48 17 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/01_min/energy_min.mdp: -------------------------------------------------------------------------------- 1 | ; min.mdp - used as input into grompp to generate em.tpr 2 | ; Parameters describing what to do, when to stop and what to save 3 | integrator = steep ; Algorithm (steep = steepest descent minimization) 4 | emtol = 100.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm 5 | emstep = 0.01 ; Energy step size 6 | nsteps = 50000 ; Maximum number of (minimization) steps to perform 7 | ;constraints = h-bonds 8 | 9 | ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 10 | nstlist = 1 ; Frequency to update the neighbor list and long range forces 11 | ns_type = grid ; Method to determine neighbor list (simple, grid) 12 | rlist = 1.4 ; Cut-off for making neighbor list (short range forces) 13 | coulombtype = PME ; Treatment of long range electrostatic interactions 14 | rcoulomb = 1.4 ; Short-range electrostatic cut-off 15 | rvdw = 1.4 ; Short-range Van der Waals cut-off 16 | pbc = xyz ; Periodic Boundary Conditions (yes/no) 17 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/02_eqm/equil_md.mdp: -------------------------------------------------------------------------------- 1 | title = MD 2 | 3 | ; Run parameters 4 | integrator = md ; leap-frog integrator 5 | nsteps = 100000 ; 1 fs * 100000 = 100 ps 6 | dt = 0.001 ; 1 fs 7 | 8 | ; Output control 9 | nstxout = 500 ; save coordinates every 1 ps 10 | nstvout = 500 ; save velocities every 1 ps 11 | nstxtcout = 500 ; xtc compressed trajectory output every 1 ps 12 | nstenergy = 500 ; save energies every 1 ps 13 | nstlog = 500 ; update log file every 1 ps 14 | 15 | ; Bond parameters 16 | constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained 17 | 18 | ; Neighborsearching 19 | ns_type = Verlet ; search neighboring grid cels 20 | nstlist = 10 ; 10 fs 21 | rlist = 1.2 ; short-range neighborlist cutoff (in nm) 22 | rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) 23 | rvdw = 1.2 ; short-range van der Waals cutoff (in nm) 24 | 25 | ; Electrostatics 26 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 27 | 28 | ; Temperature coupling is on 29 | tcoupl = vrescale ; modified Berendsen thermostat 30 | tc-grps = System ; two coupling groups - more accurate 31 | tau_t = 0.1 ; time constant, in ps 32 | ref_t = 300 ; reference temperature, one for each group, in K 33 | 34 | ; Pressure coupling is on 35 | ; Pressure coupling is on 36 | pcoupl = berendsen ; Pressure coupling on in NPT 37 | pcoupltype = isotropic ; uniform scaling of box vectors 38 | tau_p = 2.0 ; time constant, in ps 39 | ref_p = 1.0 ; reference pressure, in bar 40 | compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 41 | refcoord_scaling = com 42 | 43 | ; Periodic boundary conditions 44 | pbc = xyz ; 3-D PBC 45 | 46 | ; Velocity generation 47 | gen_vel = yes ; Velocity generation is on 48 | gen_temp = 300 ; 49 | -------------------------------------------------------------------------------- /tutorial/clayFF_example/03_prod/prod_md.mdp: -------------------------------------------------------------------------------- 1 | 2 | ; RUN CONTROL PARAMETERS 3 | integrator = sd ; sampling of the (nearly) decoupled syst should be used 4 | dt = 0.001 ; ps 5 | nsteps = 50000 ; 10000 ps = 10ns 6 | 7 | ; OUTPUT CONTROL OPTIONS 8 | nstxout = 5000 ; turn off trajectory writing; 9 | nstvout = 5000 ; turn off trajectory writing 10 | nstfout = 5000 11 | nstlog = 5000 ; Output frequency to write energies to log file 12 | nstenergy = 5000 ; Output frequency to write energies to energy file 13 | energygrps = System ; groups to write to energy file 14 | 15 | ; NEIGHBOR SEARCHING PARAMETERS 16 | nstlist = 5 ; update frequency 17 | ns_type = grid ; algorithm (simple or grid) 18 | pbc = xyz 19 | rlist = 1.4 ; cut-off distance nm 20 | 21 | ; OPTIONS FOR ELECTROSTATICS 22 | coulombtype = PME ; Method for doing electrostatics 23 | rcoulomb = 1.4 ; Coulomb cut-off distance nm 24 | 25 | ; VDW 26 | ;vdw-type = Cut-off ; Method for doing VDW 27 | rvdw = 1.4 ; cut-off lengths nm 28 | ;rvdw-switch = 1.39 29 | ;DispCorr = no ; Apply long range dispersion corrections for Energy & Pressure (EnerPres) 30 | 31 | ; OPTIONS FOR WEAK COUPLING ALGORITHMS 32 | Tcoupl = V-rescale ; Temperature coupling 33 | Tc-grps = System ; Groups to couple separately 34 | tau_T = 1.0 ; Time constant (ps) 35 | ref_T = 300 ; Reference temperature (K) 36 | 37 | ; OPTIONS FOR BONDS 38 | constraints = h-bonds 39 | ;constraint-algorithm = Lincs 40 | ;unconstrained-start = yes 41 | ;lincs-order = 4 42 | ;lincs-warnangle = 30 43 | ;lincs-iter = 8 44 | 45 | ;GENERATE VELOCITES 46 | ;gen_vel = no ; generates velocities 47 | ;gen_temp = 300 48 | ;gen_seed = 173529 49 | 50 | --------------------------------------------------------------------------------