[gmx-users] diffusion, g_msd and trestart
chees at nus.edu.sg
Mon Jul 27 11:31:29 CEST 2009
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
Sent: Monday, July 27, 2009 5:12 PM
To: Discussion list for GROMACS users
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
> I then calculate the average and the stdev:
> 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.
My simulation is 10ns long with xtc saved every 1 ps. I thought I had
How long is "long time"?
> Also, what is the reason for the trestart=10 default value? Shouldn't
> 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.
So, I must run velocity autocorrelation to find out when the velocities
become uncorrelated, and then use this time as my trestart?
> 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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