[gmx-developers] Question: Crystal symmetry support?

Berk Hess hess at kth.se
Fri Mar 9 16:17:02 CET 2012

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.

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

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