[gmx-users] g_msd

[David van der Spoel]

Arneh Babakhani wrote:
> Hi everyone, quick question about g_msd,
> 
> When I execute:   *g_msd -f FullMD1.trr -s FullMD1.tpr -n 
> ForDiffusion.ndx -o test -lateral z*
> 
> At the end, the following is outputted in my terminal:
> 
> *D[   Protein] 0.1207 (+/- 0.0847) 1e-5 cm^2/s*
> 
> My index file only contains one group, labeled Protein.  So is this 
> number, *0.1207*, the MSD of the entire group Protein? Or is this the 
> average (over the atoms) MSD in the group Protein?  (I think the latter 
> is the case, b/c in the manual, it's stated that g_msd computes the MSD 
> of atoms . . . just double-checking).

it is the average. for something as large as a protein you would prefer 
to have the center-of-mass diffusion. This is not implemented unfortunately.
> 
> Thanks much,
> 
> Arneh
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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