This repo contains a collection of scripts for generating LAMMPS input (topology files and run scripts) for simulations of methane and carbon dioxide in MOF-74 and MOF-274 frameworks using the DFT-derived FF Mercado et al. (2016). These scripts are related to MD simulations carried out for the following works: Witherspoon et al. (2019) and Forse et al. (2018). For details on the force field parameters used, see this repo.
The way the main scripts in this repo (which are titled create-LAMMPS-input-*.sh) are intended to be used is to create, for each set of simulation conditions specified, a .tcl script for putting a specific number of guest molecules in a simulation box by reading isotherm data in isothermData-74/. This .tcl script is then run using vmd to generate:
- *.data
- *.in
- and *.in.settings files.
The script works by reading:
- a template.in file
- PDB structures for frameworks (located in frameworkStructures/)
- XYZ structures for guest molecules (located in adsorbateStructures/)
- and force field parameters (defined in forceFieldParamsTemplates/).
A different set of force field template files are read depending on if the adsorbate molecule is charged or uncharged.
The instructions below are for generating input files for MD simulations of carbon dioxide in MOF-74, but analogous instructions can be followed for methane as the adsorbate and MOF-274 as the adsorbant.
To generate LAMMPS input files for carbon dioxide adsorbed in MOF-74, you can run the following script:
./create-LAMMPS-input-74-CO2.sh
Before running, define the "list" of pressures and metal frameworks that you want to create input files for at the top of create-LAMMPS-input-74-CO2.sh. This script will read the respective files from:
- the isothermData-74/ directory (to know how many gas molecules to put in the simulation box)
- the topoScripts/ directory (for the .tcl template scripts that it uses to generate the LAMMPS topology files)
- and the forceFieldParamsTemplates/ directory (for the DFT-FF parameters/charges).
template.in is the file that serves as the template for all the LAMMPS input scripts, so any changes made here will then affect all the input files generated (this is a good place to change any fixes or dump commands, but note that it contains many substrings that the create-LAMMPS-input scripts search and replace, so be careful).
As mentioned above, the analogous scripts can be used to generate input files for simulations of carbon dioxide adsorbed in MOF-274 frameworks, or for methane adsorbed in MOF-74.
I apologize for the poor documentation in this repo, especially the create-LAMMPS-input-{74-CO2, 74-CH4, 274-CO2}.sh scripts; they are functional but messy. If you spot any glaring errors, please reach out and I will be happy to fix them.
Rocío Mercado