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From: Tom Kurtzman <simpleliquid.gmail.com>

Date: Thu, 20 Dec 2018 08:13:30 -0500

Nicely said Saeed. Just adding that you can also integrate the velocity

autocorrelation function (only in unthermostatted systems) to obtain the

diffusion coefficient (Green-Kubo relationship). Both methods (Einstein

and Green-Kubo) are exact (you still will have sampling error) and provide

a good check that the calculation is being done correctly.

the derivation of the Green-Kubo relationship for diffusion also, for me,

provides the most intuitive explanation as to why the diffusion coefficient

is affected by thermostats.

Best,

Tom

On Wed, Dec 19, 2018 at 3:52 PM Saeed Izadi <izadi.vt.edu> wrote:

*> 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
*

*> >
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

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

*>
*

Date: Thu, 20 Dec 2018 08:13:30 -0500

Nicely said Saeed. Just adding that you can also integrate the velocity

autocorrelation function (only in unthermostatted systems) to obtain the

diffusion coefficient (Green-Kubo relationship). Both methods (Einstein

and Green-Kubo) are exact (you still will have sampling error) and provide

a good check that the calculation is being done correctly.

the derivation of the Green-Kubo relationship for diffusion also, for me,

provides the most intuitive explanation as to why the diffusion coefficient

is affected by thermostats.

Best,

Tom

On Wed, Dec 19, 2018 at 3:52 PM Saeed Izadi <izadi.vt.edu> wrote:

-- ************************************************ Tom Kurtzman, Ph.D. Associate Professor Department of Chemistry Lehman College, CUNY 250 Bedford Park Blvd. West Bronx, New York 10468 718-960-8832 http://www.lehman.edu/faculty/tkurtzman/ <http://www.lehman.edu/faculty/tkurtzman/index.html> ************************************************ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Dec 20 2018 - 05:30:02 PST

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