[gmx-users] infinitive force acting on atom during

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jan 15 12:53:44 CET 2007

Hi Joern,

In any case, you want to first perform an energy minimization in
vacuum to release the strain present in your starting structure. Only
then can you be sure that if you run into trouble after solvating your
system, it is caused by that. It may be that during solvation a
solvent molecule is misplaced, but that would more likely cause a
"water molecule ... cannot be settled" error. At this point, I would
suggest to introduce an additional step of energy minimization prior
to solvation. If you still run into trouble then, post again with new
details and we can have a more thorough look.

> Have you or anyone else got an idea of what goes wrong in my simulation?
> And another thing is (perhaps a stupid question ?!?): why is it better not to
> use a cubic box for the simulation ?

Not a stupid question. For one thing, the cubic box is a waste of
resources. The rhombic dodecahedron will give you the same minimum
distance between periodic images for 71% of the volume. There's an
additional advantage when using a rhombic dodecahedron. Because it
corresponds to the densest packing of a sphere, it ensures that you
have the same distribution of solvent all around your solute. With a
cubic box (or a rectangular box, or a truncated octahedron), you have
an uneven distribution and this can potentially affect the results
obtained from your simulation.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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