[gmx-users] configuration of system for small molecule crystal simulations

Vik Bajaj vikbajaj at gmail.com
Mon Sep 25 17:24:25 CEST 2006


I am attempting to simulate a small molecule in an orthorhombic unit
cell with z=4;  there is no solvent.  In this case, the crystal
packing forces are largely responsible for the molecular conformation,
and therefore the symmetry representation is critical.  I have put the
molecule in a triclinic box with dimensions equal to the lattice
dimensions, and I am not certain that this will result in appropriate
boundary conditions.  My simulation is currently blowing up, so I am
revisiting the initial setup and minimization.

If someone can clarify or provide an example of a similar problem, I
would appreciate it very much.


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