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.
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 programsFor 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 -eNote 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.
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}
}