ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

Parameters
ASE Manual, Release 3.6.1.2828
The description of the parameters can be found in the Gromacs manual:
http://www.gromacs.org/Documentation/Manual
except these parameters should be fixed: integrator = ‘md’, nsteps = ‘0’
and extra (ie non-gromacs) parameter:
init_structure_file: str The name of the initial structure file. The structure file should be in .gro format because
pdb reading in ASE is not very good.
Example1: Geometry Optimization of a histidine molecule
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
First generate the initial structure in gromacs format (.gro)
pdb2gmx -f his.pdb -o hish.gro -ff oplsaa -water tip3p
Then setup a periodic simulation box
editconf_d -f hish.gro -o hishBOX.gro -box 3 3 3
Finally, relax the structure: The sample file:
#!/usr/bin/env python
""" An example for using gromacs calculator in ase.
Atom positions are relaxed.
A sample call:
"""
./gromacs_example_relax.py hishBOX.gro
from ase import Atoms
from ase.visualize import view
from ase.calculators.gromacs import Gromacs
from ase.optimize import BFGS
from ase.optimize.bfgslinesearch import BFGSLineSearch
from ase.optimize import MDMin
from ase.optimize.sciopt import SciPyFminBFGS, SciPyFminCG
from ase.optimize.sciopt import SciPyFmin
from ase.optimize.sciopt import SciPyOptimizer
import sys
from ase.io import read, write
from ase import units
7.14. Calculators 135