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,
Tsjerk
On 9/25/06, Vik Bajaj <[EMAIL PROTECTED]> 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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