The rotation you describe can (and arguably *will*) happen for orthorhombic
boxes. This is one reason to use a truncated octahedron (or some other)
cell instead. For short simulations (~100 ns perhaps?) this may not be
obvious.
Regards,
Brian
On Fri, May 30, 2014 at 11:35 AM, Paulsen, Janet <Janet.Paulsen.umassmed.edu
> wrote:
> Dear Amber Users,
>
> When running an MD is the water “buffer zone” maintained on all sides of
> your protein? For example, if you have a period box with dimensions
> 63x55x78 angstroms and the van der waals radius of your protein is 44x35x59
> angstroms would you ever encounter a situation where the protein rotated
> and now the long edge of your protein is aligned with the short edge of the
> box and you would have a potential interaction with the periodic image. I
> have not seen this happen but the question has been posed. Any insight
> would be appreciated.
>
> Janet Paulsen
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Fri May 30 2014 - 09:00:04 PDT
