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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