Re: [AMBER] Problems calculating self diffusion coefficient of water

From: Saeed Izadi <>
Date: Wed, 19 Dec 2018 12:52:06 -0800

Hi Lucas,

What type of ensemble are you using for the calculation? .. note that
unlike many other properties of water which are calculated in NPT ensemble,
self-diffusion coefficient is safer to be estimated with no thermostat
(i.e., NVE ensemble). The use of a thermostat affects how the water
molecules move, usually leading to under estimation of self-diffusion
value. To make sure the system’s temperature does not deviate from the
target temperature, it is suggested to run a large number of short (NVE)
simulations starting from well- equilibrated evenly spaced NPT-sampled
coordinates and velocities as initial conditions. The Einstein relation can
then be used to infer the diffusion constant from the time dependence of
the mean-squared displacement, and then final value of the self-diffusion
coefficient can be obtained by averaging over all the NVE trajectories. You
can also take a look at the following paper for more information:


On Wed, Dec 19, 2018 at 9:14 AM Lucas Bandeira <>

> Hello,
> I'm trying to calculate the self coefficient diffusion of water using the
> FF TIP3P. I know that to TIP3P the value of the diffusion coefficient of
> water is different than the obtained experimentally, 5.19 * 10⁻⁹ m²*s⁻¹
> instead of 2.3 * 10⁻⁹ m² * s⁻¹, but when I try to calculated the diffusion
> coefficient I get the value 4.21 * 10⁻⁹ m² * s⁻¹. I'm using the formula on
> AMBER Manual:
> [image: image.png]
> Using n = 3. The MSD value I compute using the out_r.xmgr generated when I
> use cpptraj.
> My input looks like:
> diffusion :WAT.O 0.2 out
> I'm using Amber14 so I can't calculate diffusion coefficient directly.
> Thank you in advance,
> Lucas
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Received on Wed Dec 19 2018 - 13:00:02 PST
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