Generate Gromacs Input Files

input.py is a convenience script that will generate a GROMACS topology, given an initial configuration, as well as .mdp files. Always check that the files are accurate before using them.

input.py calls the classes defined on the following pages:

• Generate Gromacs Topology File
• Generate Gromacs .mdp Files

Command Line Functionality

To use the script, run it from the command line with the following usage.

usage: input.py [-h] [-T TITLE] [-b BUILD_MON] [-s EM_STEPS] [-e ENSEMBLE]
                [-d DT] [-l LENGTH] [-f FRAMES] [-p PCOUPLTYPE]
                [--restraints RESTRAINTS [RESTRAINTS ...]] [-x] [-c COORD]
                [-S] [--temp TEMP] [--mdp] [--barostat BAROSTAT] [--nogenvel]
                [--bcc] [--solvent SOLVENT] [--tau_t TAU_T] [--tau_p TAU_P]
                [-nx NSTXOUT] [-nv NSTVOUT] [-nf NSTFOUT] [-ne NSTENERGY]

Named Arguments

-T, --title	Simulation Title Default: “Generic Molecular Dynamics Simulation”
-b, --build_mon
	Monomer structure used for build Default: “NAcarb11V”
-s, --em_steps	Steps to take during energy minimization Default: -1
-e, --ensemble	Thermodynamic ensemble to put system in Default: “npt”
-d, --dt	time step (ps) Default: 0.002
-l, --length	simulation length (ps) Default: 1000
-f, --frames	number of frames Default: 500
-p, --pcoupltype
	Pressure Couple Type Default: “semiisotropic”
--restraints	Specify residue for which restraints are specified
-x, --xlink	Turn this to “on” if the the system is crosslinked Default: False
-c, --coord	coordinate file of system to be simulated Default: “initial.gro”
-S, --solvate	Specify this if the system has water so an extra line can be added to the topology Default: False
--temp	Specify temperature at which to run simulation Default: 300
--mdp	Only the .mdp will be written if this option is specified Default: False
--barostat	pressure coupling scheme to use Default: “berendsen”
--nogenvel	Do not generate velocities Default: True
--bcc	Generate input files using bicontinuous cubic files Default: False
--solvent	Name of solvent Default: “water”
--tau_t	Temperature coupling time constant Default: 0.1
--tau_p	Pressure coupling time constant Default: 20
-nx, --nstxout	Frequency to output coordinates to trajectory file
-nv, --nstvout	Frequency to output velocities to trajectory file
-nf, --nstfout	Frequency to output forces to trajectory file
-ne, --nstenergy
	Frequency to output energy to energy file