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From: Saeed Izadi <izadi.vt.edu>

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:

https://onlinelibrary.wiley.com/doi/full/10.1002/wcms.1347

best,

Saeed

On Wed, Dec 19, 2018 at 9:14 AM Lucas Bandeira <bandeiralucas97.gmail.com>

wrote:

*> 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
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

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

*>
*

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Received on Wed Dec 19 2018 - 13:00:02 PST

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:

https://onlinelibrary.wiley.com/doi/full/10.1002/wcms.1347

best,

Saeed

On Wed, Dec 19, 2018 at 9:14 AM Lucas Bandeira <bandeiralucas97.gmail.com>

wrote:

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Received on Wed Dec 19 2018 - 13:00:02 PST

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