[gmx-users] g_msd

Kay Gottschalk kay.gottschalk at weizmann.ac.il
Fri Jun 27 11:51:01 CEST 2003

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...

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