John,
To my knowledge, the only place that AMBER learns about system volume is in
the coordinate file, the last line of which contains the lattice lengths
and angles (a, b, c, alpha, beta, gamma). So long as your system already
has the correct shape you can just re-assign the lengths manually. There
is also a program in $AMBERHOME/bin called ChBox that will do this
automatically, but I'm not certain of its usage/quality.
If you are expanding your volume, then additional dynamics is generally
stable in my experience. If you are contracting your volume, then things
might get messy. I would recommend running constant pressure dynamics
before shrinking the volume, as systems with negative virial will rapidly
contract the simulation cell in general.
Regards,
Brian
On Wed, Jan 18, 2012 at 8:28 AM, Beale, John <John.Beale.stlcop.edu> wrote:
>
> I need to adjust the density of my protein/explicit water system to match
> experimental density values at a variety of temperatures. From what I have
> read, to do this I should adjust the volume of the system. Can someone
> please tell me how to do this?
>
> John
>
> John M. Beale, Jr., Ph.D.
> Professor of Medicinal Chemistry and Pharmacognosy
> Saint Louis College of Pharmacy
> 4588 Parkview Place
> Saint Louis, Missouri 63110-1088
> Office: 314-446-8461
> Cell: 314-315-0409
> FAX: 314-446-8460
> John.Beale.stlcop.edu<mailto:John.Beale.stlcop.edu>
>
>
>
>
> _______________________________________________
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> 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 Wed Jan 18 2012 - 06:00:05 PST
