[gmx-users] Simulating crystal structures

[Dallas Warren]

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

http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-periodic-molecules

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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