[AMBER] Problems calculating self diffusion coefficient of water

From: Lucas Bandeira <bandeiralucas97.gmail.com>
Date: Wed, 19 Dec 2018 15:13:07 -0200


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,


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(image/png attachment: image.png)

Received on Wed Dec 19 2018 - 09:30:02 PST
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