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

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Sep 26 10:07:06 CEST 2006

Hi Vik,

Did you make sure the (rotational) orientation of your molecule
corresponded to the triclinic unit cell? And did you visualize the
crystal (using e.g. genconf to extend the system)?

Hope it helps,


On 9/25/06, Vik Bajaj <vikbajaj at gmail.com> wrote:
> Hello,
> 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.
> -Vik
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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