[gmx-users] g_msd and Diffusion Constant

Ganesh Shahane ganesh7shahane at gmail.com
Mon Jul 20 13:28:26 CEST 2015

Dear Gromacs Users,

I have performed a simulation of a POPC+Cholesterol bilayer. I wish to know
the diffusion constant of a particular cholesterol molecule. Towards this,
I performed a g_msd using the command as follows-

g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 800000 -n index.ndx -mol

where index.ndx contains a single index for the cholesterol atoms in
question. In the end, I got 2 different values of diffusion constant, with
one of them being displayed on the terminal screen and the other value in
the chol.xvg file.

Does anyone have any idea as to which value should be taken as the value of
diffusion constant? Any help would be appreciated. Thank you!

Best Regards,
Ganesh Shahane

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