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From: Lucas Bandeira <bandeiralucas97.gmail.com>

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

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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AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

(image/png attachment: image.png)

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