[gmx-users] (no subject) - fluctuations

[Antonia V.]

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.

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.
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