[gmx-users] diffusion, g_msd and trestart

[David van der Spoel]

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, 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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> 
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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