[gmx-users] RE: msd vs. time plot for molecules

Vitaly Chaban vvchaban at gmail.com
Fri Jun 20 21:51:31 CEST 2008

> Using g_msd on a group of atoms results in an msd vs. time plot which is
> the result of an average over all the atoms' motions.  I would like to 
> obtain the same plot, but for an average over the center of mass motions 
> of a group of molecules.  Using the -mol option results in a plot of the 
> diffusion coefficient for each individual molecule.  Do I need to use 
> the -mw option for each molecule seperately and then average them 
> together myself?  Thank you for any ideas.
It seems that because MSDs of separate atoms are mostly very close to those
of the center-of-mass GROMACS developers has made the latter case
default. Using the '-mol' of g_msd option should give
you a diffusion constant of the center-of-mass (besides that graph)...

I'm not sure, however. It's also a good idea to examine a programme
code. :)

Vitaly V. Chaban
School of Chemistry
University of Kharkiv
Svobody sq.,4
Kharkiv 61077, Ukraine

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