[gmx-users] g_msd

David spoel at xray.bmc.uu.se
Fri Jun 27 12:01:03 CEST 2003

On Fri, 2003-06-27 at 11:50, Kay Gottschalk wrote:
> Hi there,
> I want to calculate the mean square displacement for each individual of 
> my water molecules in steps of 2 ps - would something like g_msd -mol 
> -trestart 2 do that?? That would mean, that I get 250 different 
> displacements for a 500 ps simulation, if I am not mistaken (at least 
> that's what I want). Or does it average all these 250 different 
> displacements? What is also kind of unfortunate is that I get a 'bus 
> error' when I do  'g_msd -f full -s full -mol -trestart 2'. Why might 
> that be? I'm afraid I don't really understand what I am doing with 
> g_msd and which options I have...

a little detail is that g_msd expects "molecule" numbers in the index
file with the -mol flag, so for your average 216 spc box, you'd have
numbers 1 through 216

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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel

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