The subject of barostats has been discussed for many years now on this
listserv. Negative values of the *instantaneous* pressure just indicate
that it is favorable for the system to be compressed. The large changes are
just a consequence of the fact that the P-V isotherms are very steep
(*i.e.*the density of aqueous systems don't really change that much at
constant
temperature unless the pressure changes a LOT).
Of course none of this really has anything to do with the force fields
predicting "good" densities, especially for things that aren't water. You
might want to look at the recent PNAS paper by Chen and Garcia looking at,
amongst other things, nucleotide aggregation (FF10 didn't do so hot as I
recall).
Brian
On Fri, May 9, 2014 at 11:32 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, 2014-05-09 at 19:49 +0530, Sourav Purohit wrote:
> > Even After 50 ns long NPT simulation I saw that the pressure values are
> all
> > negative and fluctuating about -500. The system consists of a large
> number
> > of DNA fragments initially arranged in a crystal with a water buffer of
> 30
> > Ang.. I wanted to see the type of LC phase the system attains.
> > The density also attained a large value.
> > I had heard from my colleagues about similar problems with multinode
> > multigpu NPT simulations. I just wanted to make sure that all the results
> > that I get are right. Do you feel that the observations of a high density
> > and negative pressure even after a long run are okay for the system I am
> > simulating?? Kindly help.
>
> I have no idea. I haven't run a multi-node GPU NPT simulation before.
>
> Try doing a density equilibration on the CPU (or a single GPU) and see
> if the results you get there match the results you get with the
> multi-node GPU. (It should not take 50 ns to equilibrate your density)
>
> BTW, you also have to tell us what version of Amber you are using for
> the best help, as well as which updates have been applied. This is
> always a good idea. (And make sure that all updates have been applied;
> although currently this only applies to Amber 12).
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> 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 09 2014 - 09:30:02 PDT
