Enemark Soeren wrote:
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@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
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.
My simulation is 10ns long with xtc saved every 1 ps. I thought I had
enough data!?
How long is "long time"?
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.
So, I must run velocity autocorrelation to find out when the velocities
become uncorrelated, and then use this time as my trestart?
.
That would be a way (and the VACF also gives you a diffusion constant),
you can also check the histogram visually for different run times. It
seems that your solution does have a lot of amino acids, which probably
means high viscosity and slow diffusion, and hence long time to
equilibrate. Looking at the system MSD for all the Gly may also show you
when the MSD curve becomes linear, you can use this as well as an
estimate for the trestart.
Thanks,
Soren
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.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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