From: Radak, Brian K (bradak_at_anl.gov)
Date: Mon Jul 25 2016 - 12:48:13 CDT
I don't think that most common formulations for self diffusion coefficients expect periodic boundaries. Maybe using the velocity autocorrelation would avoid this?
The easiest solution is almost certainly to use "wrapAll off" or else "unwrap" the trajectory somehow (using VMD perhaps?).
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From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Mahdiye Azadpour [azadpour.mahdiyeh_at_gmail.com]
Sent: Saturday, July 23, 2016 11:21 PM
Subject: namd-l: Msd
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 experimental.
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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