Re: [AMBER] help in calculating diffusion coefficient

From: David A Case <>
Date: Mon, 8 Dec 2014 10:00:58 -0500

On Mon, Dec 08, 2014, Robin Jain wrote:

> I am new in MD and i have simulated a organic molecule in 80 methanol and i
> have equilibrated my system for about 5ns . Now i want to calculate the
> diffusion coefficient, therefore what should i do and how, so please help
> me in this regard.

Please look at the "diffusion" keyword in the cpptraj section of the manual.

However, if by "80 methanol", you mean 80 methanol molecules as solvent, that
is not nearly enough. You would need several thousand solvent molecule in a
periodic simulation in order to study diffusional behavior. Note also that
you will need to either do an NVE simulation (following NTP equilibration) or
at least us a very weak coupling thermostat (ntt=1) in order to study
dynamical properites.

....hope this helps...dac

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Received on Mon Dec 08 2014 - 07:30:02 PST
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