[gmx-developers] Question: Crystal symmetry support?

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Mar 9 16:25:33 CET 2012

One interesting crystal symmetry that cannot be simulated (as far as I  
know) is P2sub1(-x,y+1/2,-z), which would allow lipids to move out of  
one leaflet into the other leaflet across PBC and thus equilibrate  
area per lipid across both leaflets without lipid flip-flop in the  
conventional sense (  
). It has been implemented in charmm (Dolan, Venable, Pastor, and  
Brooks Biophys. J. Vol. 82 May 2002, 2313-2325).

Quoting Berk Hess <hess at kth.se>:

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