[gmx-users] When crystal dimension is less than rcoulomb and rlist

David van der Spoel spoel at xray.bmc.uu.se
Sun Dec 8 21:43:36 CET 2013

On 2013-12-08 21:12, Golshan Hejazi wrote:
> Hello everyone,
> I am trying to compute the energy of a crystal slab using steepest decent. Learning from previous questions in the group. I am using pbc in all direction. I need to compute this energy for one layer of crystal. Since crystal unit cell vectors (a b and c) can be less than rcoulomb and rlist ... it is obvious that I receive error while generating the tpr file.
> as an example, lets assume that a=0.7, b=.9 and c=1.1 angstrom, this means if I have a crystal slab of face(100), and b and c are in XY plane, then box dimension along z axes which is equal to 0.7 ... is less than rlist ...
> how can i compute the energy of a crystal slab then? If I decrease rcoulomb and rlist ... I am introducing artifact in computing electrostatic interaction and obviously, I can not increase box dimension along Z because in that way, crystal wont be periodic along Z anymore.
> Best and thanks for you useful comments in advance
> G.
Use multiple layers and divide by the number of layers.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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