[gmx-users] Simulating crystal structures

Dallas Warren dallas.warren at monash.edu
Mon Aug 6 00:37:21 CEST 2018

You need to use this option for molecules that go over the PBC


Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Fri, 3 Aug 2018 at 03:38, 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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