From: Mahdiye Azadpour (
Date: Sat Jul 23 2016 - 23:21:09 CDT

I simulated pure gas methane to calculated self diffusion coefficient.
I wrote scripts to calculateed self diffusion coefficient methane also used
plugin msd. But is very different than experimental data.

My system is pure methane. I used CHARMM force feild. I run npt for 3 ns
after equilibrium I Calculated volume. Density of methane gas equal

I used pdb file in lastest frame to input nvt and v has equaled volume in
npt run. I used periodic boundary conditions.

When I used wrap all on. My msd is nonlinear. After I used wrap all off my
msd is linear. Both method my Calculation self diffusion coefficient
completely different with experimental data.
How can I run for msd?

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