[gmx-users] Diffusion by g_msd

Alok Jain alokjain16 at gmail.com
Mon Jan 25 14:13:31 CET 2010

Dear All,

I was trying to calculate diffusion of water molecule in a membrane
channel protein by g_msd utility of gromacs.

First I have identified channel waters which reside inside the channel
for 500ps (5000ps-5500ps simulation time).

Letter I have made a index file specifying these water molecules.

my input command was g_msd -f XXX.xtc -s XXX.tpr -n index.ndx -o msd.xvg
-type z -trestart 20 -b 5001 -e 5500

My question it is the correct way to calculate the diffusion for my
desired water molecule within desired time?


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