[gmx-users] Simulating crystal structures

Momin Ahmad momin.ahmad at kit.edu
Thu Aug 2 19:38:27 CEST 2018


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


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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