[gmx-users] Fwd: Diffusion of protein

neha bharti nehabharty123 at gmail.com
Wed Sep 23 07:40:52 CEST 2015

Hello all

I am trying to performed molecular dynamics simulation of ligand-protein
complex in popc lipid with charmm36 force field. I am taking help from
Justin A. Lemkul tutorial.

I wanted to calculate the diffusion of the protein. Before performing the
study I removed the PBC of my system.
I am using msd command

*g_msd -f md_whole.xtc -s md.tpr  -b 0 -e 100000 -o diffusion.xvg*

but the graph is not a straight line

[image: Inline image 1]

when I am using g_analyse after g_msd command i.e. *g_analyze -f
diffusion.xvg -msd diffusion_analyze.xvg *the graph is straight line  but
the graph is showing only for 50 ns (half of the simulation time)

Can anyone please tell me which graph should I refer. Or I am doing
something wrong??

Is there any other command to calculate the diffusion?

Please help

With Regards
Neha bharty

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