[gmx-developers] Question: Crystal symmetry support?

[David van der Spoel]

On 2012-03-09 16:48, Shirts, Michael (mrs5pt) wrote:
>> 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.
>
> Absolutely, agreed.  Note that with small molecules, this getting one (or
> multiple unit cells wouldn't be that bad).
>
>> As we support general triclinic cells, any crystal can be simulated.
>> Simulating only one copy will almost never work, as this would
>> introduce singularities.
>
> OK, then perhaps we should be thinking about ways to automate the setup for
> different space groups?  I'm happy to look at this (with others, if there is
> additional interest), though that will be a bit lower on my priority list.
>
? Unit cell detection from a pdb file works fine. What do you want to add?

> 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