[gmx-developers] Question: Crystal symmetry support?

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 9 16:24:40 CET 2012

On 2012-03-09 16:17, Berk Hess wrote:
> On 03/09/2012 04:11 PM, Shirts, Michael (mrs5pt) wrote:
>>>> Just wondering -- is there anyone out there looking at support for
>>>> simulating with protein crystal symmetry? Is it in there already, and I
>>>> haven't noticed?
>>> There are almost no crystal symmetries you can simulate, if I understood
>>> correctly what you mean.
>>> For energy minimization you can use symmetries, but any fluctuations
>>> should not be symmetric.
>> Sorry for not being clearer -- I meant, simulations in which one could
>> actually simulate the crystal symmetric cell, such
>> as P 2(1)2(1)2(1) and P 2(1). This would allow actually studying the
>> naturally occurring crystallographic contacts, though of course if
>> only one
>> symmetric cell was simulated, then the fluctuation spectrum would not be
>> correct.
> As we support general triclinic cells, any crystal can be simulated.
> Simulating only one copy will almost never work, as this would
> introduce singularities.

Problem is that you need at least one entire unit-cell, so you can not 
use symmetry to simulate only one protein instead of 8 in a P212121 cell.

> Berk
>> Best,
>> ~~~~~~~~~~~~
>> Michael Shirts
>> Assistant Professor
>> Department of Chemical Engineering
>> University of Virginia
>> michael.shirts at virginia.edu
>> (434)-243-1821

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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