[gmx-users] Fwd: Diffusion of protein
nehabharty123 at gmail.com
Wed Sep 23 07:40:52 CEST 2015
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
Is there any other command to calculate the diffusion?
More information about the gromacs.org_gmx-users