jrdcasa / intermol_cj

InterMol: a conversion tool for molecular dynamics simulations. I have added the possibility to use Toxvaerd potentials for *-CH2-CH2-* in GROMACS and LAMMPS ( Toxvaerd, S. J. Chem. Phys. 1997, 107, 5197). This potential is important for polyethylene segments improving the dimension chains respect to TrappeUA

InterMol: a conversion tool for molecular dynamics simulations

We are currently in beta testing phase. Desmond<=>Gromacs<=>Lammps conversions are carried out natively in InterMol. AMBER->X is carried out by converting AMBER to GROMACS, then to other programs using ParmEd. AMBER->CHARMM is carried out by ParmEd directly.

Installation instructions

Basic usage

To check out how it works, use the convert.py script found in the intermol directory:

$ python convert.py -h
usage: convert.py [-h] [--des_in file] [--gro_in file file] [--lmp_in file] [--amb_in file file] [-crm_in file] 
                  [--desmond] [--gromacs] [--lammps] [--amber] [--charmm] [--odir directory]
                  [--oname prefix] [-e] [--efile EFILE] 
                  [-dp, --despath] [-ds, --desmondsettings]
                  [-gp, --gropath path] [-gs, --gromacssettings]
                  [-lp, --lmppath] [-ls, --lammpssettings]
                  [-ap, --amberpath] [-as, --ambersettings]
                  [-cp, --charmmpath path] [-cs, --charmmsettings]
                  [-l path] [-f] [-v]

Perform a file conversion

optional arguments:
  -h, --help            show this help message and exit

Choose input conversion format:
  --amb_in file         input files (.prmtop) and (.crd or equivalent) for
                        conversion from AMBER file format
  -crm_in file          input file (.imp) for conversion from CHARMM file format
  --des_in file         .cms file for conversion from DESMOND file format
  --gro_in file file    .gro and .top file for conversion from GROMACS file
                        format
  --lmp_in file         input file for conversion from LAMMPS file format
                        (expects data file in same directory and a read_data call)
  
Choose output conversion format(s):
  --amber               convert to AMBER
  --charmm              convert to CHARMM
  --desmond             convert to DESMOND
  --gromacs             convert to GROMACS
  --lammps              convert to LAMMPS
  
  
Other optional arguments:
  --odir directory      specification of output directory (default: ./)
  --oname prefix        specification of prefix for output filenames (default:
                        inputprefix_converted)
  -e, --energy          evaluate energy of input and output files for
                        comparison
  --efile EFILE         optional run file for energy evaluation (e.g. .cfg,
                        .mdp, .input)
  -dp, --despath path
                        path for DESMOND binary, needed for energy evaluation
  -ds, --desmondsettings settings
                        Desmond .cfg settings file used for energy evaluation
  -gp, --gropath path
                        path for GROMACS binary, needed for energy evaluation
  -gs, --gromacssettings settings
                        Gromacs .mdp settings file used for energy evaluation
  -lp, --lmppath path
                        path for LAMMPS binary, needed for energy evaluation
  -ls, --lammpssettings settings
                        pair_style string to use in the output file. Default
                        is a periodic Ewald simulation
  -ap, --amberpath path
                        path for AMBER binary, needed for energy evaluation
  -as, --ambersettings settings
                        AMBER .in file used for energy evaluation
  -cp, --charmmpath path
                        path for CHARMM binary, needed for energy evaluation
  -cs, --charmmsettings settings
                        CHARMM .in settings used for energy evaluation.
                        Because of the unified input file, settings lines
                        rather than a file are part


  -f, --force           ignore warnings
  -v, --verbose         high verbosity, includes DEBUG level output
  -n, --noncanonical    print the 'noncanonical' enery terms, the ones that
                        only occur in 1 or 2 programs

For example, to convert from desmond to gromacs and evalutate the energy of the input and output files:

mkdir test_output
python convert.py --des_in validation/inputs/Desmond/UnitTest/frag_opls2001/frag_opls2001.cms --gromacs --odir test_output -e

Note that the program may not give the same ASCII output; the goal is to produce the same energy output, and there are frequently multiple ways to express the same molecular potential energy function using differently formatted files.

We're also developing a comprehensive test suite to ensure that all InterMol conversions happen correctly. For instructions on how to run this check out the testing README.

Citation

InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:

@article{shirts2016lessons,
  title={Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset},
  author={Shirts, Michael R and Klein, Christoph and Swails, Jason M and Yin, Jian and Gilson, Michael K and Mobley, David L and Case, David A and Zhong, Ellen D},
  journal={Journal of computer-aided molecular design},
  pages={1--15},
  year={2016},
  doi={doi:10.1007/s10822-016-9977-1}
  publisher={Springer International Publishing}
}