Gromacs

Introduction

Gromacs is a free classical molecular dynamics package. It is mainly used in modeling of biological systems. It is part of the ubuntu-linux distribution. http://www.gromacs.org/

Warning

  1. Ase-Gromacs calculator works properly only with gromacs version 4.5.6 or a newer one. (fixed bug related to .g96 format)

Warning

  1. It only makes sense to use ase-gromacs for qm/mm or for testing. For pure MM production runs the native gromacs is much much faster (at the moment ase-gromacs has formatted io using .g96 format which is slow).

Gromacs Calculator

This ASE-interface is a preliminary one and it is VERY SLOW so do not use it for production runs. It is here because of we’ll have a QM/MM calculator which is using gromacs as the MM part.

For example: (setting for the MM part of a QM/MM run, parameter ‘-nt 1’ for serial run):

CALC_MM = Gromacs(doing_qmmm = True)
CALC_MM.set_own_params_runs('extra_mdrun_parameters', ' -nt 1 ')
Here default values for MM input are::
define = ‘-DFLEXIBLE’, integrator = ‘cg’, nsteps = ‘10000’, nstfout = ‘10’, nstlog = ‘10’, nstenergy = ‘10’, nstlist = ‘10’, ns_type = ‘grid’, pbc = ‘xyz’, rlist = ‘1.15’, coulombtype = ‘PME-Switch’, rcoulomb = ‘0.8’, vdwtype = ‘shift’, rvdw = ‘0.8’, rvdw_switch = ‘0.75’, DispCorr = ‘Ener’
The input values can be changed by::
CALC_MM.set_own_params(
‘nsteps’,‘99999’ ‘Number of steps’)
The arguments for gromacs programs can be changed by::
CALC_MM.set_own_params_runs(
‘extra_pdb2gmx_parameters’,’-ignh’)
CALC_MM.set_own_params_runs(
‘init_structure’,‘1GM2.pdb’)
CALC_MM.set_own_params_runs(
‘extra_mdrun_parameters’, ‘ -nt 1 ‘)
CALC_MM.set_own_params_runs(
‘extra_grompp_parameters’, ‘ ‘)
CALC_MM.set_own_params_runs(
‘extra_editconf_parameters’, ‘ ‘)
CALC_MM.set_own_params_runs(
‘extra_genbox_parameters’, ‘ ‘)

Parameters

The description of the parameters can be found in the Gromacs manual: http://www.gromacs.org/Documentation/Manual

and extra (ie. non-gromacs) parameter:

do_qmmm: logical (default False)
If true we run only single step of gromacs (to get MM forces and energies in QM/MM)
freeze_qm: logical (default False)
If true, the qm atoms will be kept fixed (The list of qm atoms is taken from file ‘index_filename’, below)
clean: logical (default True)
If true old gromacs files are cleaned
force_field: str (default oplsaa)
Name of the force field for gromacs
water_model: str (default tip3p)
Name of the water model for gromacs

Environmental variables:

  • GMXCMD the name of the main gromacs executable (usually ‘mdrun’). If GMXCMD is not set gromacs test is not run, but in the calculator works using ‘mdrun’.
  • GMXCMD_PREF prefix for all gromacs commands (default ”)
  • GMXCMD_POST postfix (ie suffix) for all gromacs commands (default ”)

Example: MM-only geometry optimization of a histidine molecule

THIS IS NOT A PROPER WAY TO SETUP YOUR MD SIMULATION. THIS IS JUST A DEMO THAT DOES NOT CRASH. (the box size should be iterated by md-NTP, total charge should be 0).

Initial pdb coordinates (file his.pdb):

COMPND HIS HISTIDINE
REMARK HIS Part of HIC-Up: http://xray.bmc.uu.se/hicup
REMARK HIS Extracted from PDB file pdb1wpu.ent
HETATM    1  N   HIS  4234       0.999  -1.683  -0.097  1.00 20.00      
HETATM    2  CA  HIS  4234       1.191  -0.222  -0.309  1.00 20.00      
HETATM    3  C   HIS  4234       2.641   0.213  -0.105  1.00 20.00      
HETATM    4  O   HIS  4234       3.529  -0.651  -0.222  1.00 20.00      
HETATM    5  CB  HIS  4234       0.245   0.546   0.619  1.00 20.00      
HETATM    6  CG  HIS  4234      -1.200   0.349   0.280  1.00 20.00      
HETATM    7  ND1 HIS  4234      -1.854  -0.849   0.470  1.00 20.00      
HETATM    8  CD2 HIS  4234      -2.095   1.176  -0.310  1.00 20.00      
HETATM    9  CE1 HIS  4234      -3.087  -0.752   0.006  1.00 20.00      
HETATM   10  NE2 HIS  4234      -3.258   0.467  -0.474  1.00 20.00      
HETATM   11  OXT HIS  4234       2.889   1.404   0.141  1.00 20.00      
REMARK HIS ENDHET

The sample file for relaxation:

""" An example for using gromacs calculator in ase.
    Atom positions are relaxed.
    A sample call:

   python ./gromacs_example_mm_relax.py his.pdb
"""

from ase.calculators.gromacs import Gromacs

import sys

infile_name = sys.argv[1]

CALC_MM_RELAX = Gromacs(clean=True)
CALC_MM_RELAX.set_own_params_runs(
    'extra_pdb2gmx_parameters', '-ignh')
CALC_MM_RELAX.set_own_params_runs(
    'init_structure', infile_name)
CALC_MM_RELAX.generate_topology_and_g96file()
CALC_MM_RELAX.write_input()
CALC_MM_RELAX.set_own_params_runs(
    'extra_editconf_parameters', '-bt cubic -c -d 0.8')
CALC_MM_RELAX.run_editconf()
CALC_MM_RELAX.set_own_params_runs(
    'extra_genbox_parameters', '-cs spc216.gro')
CALC_MM_RELAX.run_genbox()
CALC_MM_RELAX.generate_gromacs_run_file()
CALC_MM_RELAX.run()