[gmx-users] diffusion, g_msd and trestart

[Berk Hess]

> Date: Mon, 27 Jul 2009 11:12:16 +0200
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] diffusion, g_msd and trestart
> 
> Enemark Soeren wrote:
> > Dear all,
> > 
> > I am trying to calculate diffusion coefficients for a system of (30) 
> > glycine molecules in a box with (1000) water.
> > 
> >  
> > 
> > After running:
> > 
> > g_msd –f md.xtc –s md.tpr –mol –n molindex.ndx
> > 
> >  
> > 
> > I get a list of diffusion coefficients – one for each glycine molecule. 
> > I then calculate the average and the stdev:
> > 
> >  
> > 
> > Average=1.004
> > 
> > Stdev=0.7661
> > 
> >  
> > 
> > My problem is that the stdev is very great! More than +/- 75% of the 
> > average value.
> > 
> > Why is that?
> 
> Short simulation most likely. Since these things are big it takes a long 
> time to equilibrate.
> 

Also it depends on what you expect.
stdev is not a standard error estimate of the average.
It is the spread around the average for all molecules.
If all the msd values of the molecules are uncorrelated,
which they might or might not be, the error estimate would be stdev/sqrt(30).

Berk

> > 
> >  
> > 
> > Also, what is the reason for the trestart=10 default value? Shouldn’t it 
> > be better to have trestart=1, if my xtc file is saved every 1 ps?
> 
> No, because there is correlation in the system. Ideally you would take 
> this time to be longer than the correlation time. You could try to find 
> an estimate of that from the velocity autocorrelation.
> 
> 
> > 
> >  
> > 
> > Thanks,
> > 
> > Soren Enemark
> > 
> > 
> > ------------------------------------------------------------------------
> > 
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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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