[gmx-users] g_msd

David L. Bostick dbostick at physics.unc.edu
Fri Sep 13 21:59:13 CEST 2002


I have some questions on the usage of g_msd.  I wish to calculate the
diffusion coefficient of water.  To do this I have made an index file using
an awk script containing one group of water molecule numbers.. i.e. residue
numbers as they appear in a pdb file for water.  Are these the numbers the
manual means when I select the -mol option?

Also, what is the -trestart option for?  If I were to guess, I would say it
is the time interval over which the average msd calculation is started over
again.  Is this correct?  If this is true then -beginfit and -endfit should
be from 0 to the trestart time?  I'm kind of confused about what these
options mean.

Perhaps if someone can give me an example of how they have used it
successfully in the past, how long the trajectory was, how often snapshots
were saved, and how the command looked when they did it....

Thanks in advance,

David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

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