[gmx-users] Simulating crystal structures

Lakshman Ji Verma lakshmanjivrm at gmail.com
Tue Aug 7 05:39:16 CEST 2018

Hi Momin,

This won’t work unless you are simulating only single molecules i.e. only
unit cell with box parameters same as unit cell. Broken molecules will have
larger distances between atoms than actual bond length in a crystal
containing more than one unit cell, which will give error. So you need to
unwrap the unit cell to get whole molecule before you can replicate it to
get crystal.

If you have a correct unitcell.cif file of molecule, Chimera will be able
to wrap the molecule.


On Thu, Aug 2, 2018 at 12:38 PM Momin Ahmad <momin.ahmad at kit.edu> wrote:

> Hello,
> is GROMACS able to simulate crystaline structures properly? I have two
> residues parametrized that build up the crystal structure. The unit cell
> is however cut off at the edges (periodicity). So the question is if i
> enable periodic boundry conditions will GROMACS be able to handle the
> edges properly (covalent bonds that end on the one side are continued on
> the other side)? And is it possible to tell GROMACS that the uncomplete
> residues in the corners/edges of the unit cell are just the already
> parametrized or do i have to create another residue entry for each
> edge/corner molecules?
> Thanks in advance
> Cheers
> Momin
> --
> Momin Ahmad
> Karlsruhe Institute of Technology (KIT)
> Steinbuch Centre for Computing (SCC)
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Phone: +49 721 608-24286
> E-Mail: Momin.Ahmad at kit.edu
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