Date: Wed, 19 Dec 2018 15:13:07 -0200
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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(image/png attachment: image.png)
