[gmx-users] (no subject) - fluctuations

[Antonia V.]

artificially small???

I think I will have to read some things about Berendsen and PR.

Thanks
Antonia

> Date: Tue, 24 Mar 2009 11:09:07 +0100
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] (no subject) - fluctuations
> 
> Antonia V. wrote:
> > Hello,
> > 
> > I am interested mainly in the density.
> > When using parinello-rahman and nose-hoover the fluctuations are 
> > approximately +/- 8. But when I am using Berendsen it falls to +/- 3.
> > I wanted to know if there is a way to reduce the fluctuation width of 
> > the first case.
> 
> The density fluctuations in Berendsen are artificially small, so PR ones 
> should be more realistic. This is important when computing properties 
> like compressibility.
> 
> > 
> > Antonia
> > 
> >  > Date: Tue, 24 Mar 2009 09:49:45 +0100
> >  > From: spoel at xray.bmc.uu.se
> >  > To: gmx-users at gromacs.org
> >  > Subject: Re: [gmx-users] (no subject) - fluctuations
> >  >
> >  > Antonia V. wrote:
> >  > > Hello,
> >  > >
> >  > > So a I can either increase my system size or do some post
> >  > > precessing-smoothing...
> >  >
> >  > If you elaborate on which properties you are interested in it may be
> >  > possible to come up with more tips.
> >  > >
> >  > > Thanks for the ideas
> >  > > Antonia
> >  > >
> >  > > > Date: Tue, 24 Mar 2009 11:39:19 +1100
> >  > > > From: Dallas.Warren at pharm.monash.edu.au
> >  > > > Subject: RE: [gmx-users] (no subject) - fluctuations
> >  > > > To: gmx-users at gromacs.org
> >  > > >
> >  > > > > > Is there a way to reduce the fluctuations of the properties
> >  > > > > calculated
> >  > > > > > with g_energy?
> >  > > >
> >  > > > > Fluctuations scale as 1/sqrt(N) where N is the number of
> >  > > > > molecules. So
> >  > > > > the answer is yes.
> >  > > >
> >  > > > Depending on what you actually want to do, some smoothing of the data
> >  > > > may be what you are after. One way of doing this is taking some 
> > points
> >  > > > before and after a time, then averaging them all together.
> >  > > >
> >  > > > Catch ya,
> >  > > >
> >  > > > Dr. Dallas Warren
> >  > > > Department of Pharmaceutical Biology and Pharmacology
> >  > > > Pharmacy and Pharmaceutical Sciences, Monash University
> >  > > > 381 Royal Parade, Parkville VIC 3010
> >  > > > dallas.warren at pharm.monash.edu.au
> >  > > > +61 3 9903 9167
> >  > > > ---------------------------------
> >  > > > When the only tool you own is a hammer, every problem begins to 
> > resemble
> >  > > > a nail.
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> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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