Conversion tool for molecular simulations.
We are currently in alpha testing phase, debugging Desmond<=>Gromacs<=>Lammps conversions.
To check out how it works, use the convert.py script found in the testing directory:
$ python convert.py -h
usage: convert.py [-h] [--des_in file] [--gro_in file file] [--lmp_in file]
[--desmond] [--gromacs] [--lammps] [--odir directory]
[--oname prefix] [-e] [--efile EFILE] [-d path] [-g path]
[-l path] [-f]
Perform a file conversion
optional arguments:
-h, --help show this help message and exit
Choose input conversion 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 .lmp file for conversion from LAMMPS file format
(expects matching .input file)
Choose output conversion format(s):
--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)
-d path, --despath path
path for DESMOND binary, needed for energy evaluation
-g path, --gropath path
path for GROMACS binary, needed for energy evaluation
-l path, --lmppath path
path for LAMMPS binary, needed for energy evaluation
-f, --force ignore warnings
For example, to convert from desmond to gromacs and evalutate the energy of the input and output files:
# current working directory is Intermol/testing
mkdir test_output
python convert.py --des_in 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.