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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Fri, 21 Dec 2018 15:04:39 -0500

On Thu, Dec 20, 2018 at 8:14 AM Tom Kurtzman <simpleliquid.gmail.com> wrote:

*>
*

*> 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
*

Brief note here: due to the fact that the velocity autocorrelation

function decays pretty rapidly you have to save velocity information

more frequently than you coordinate information when using the

Einstein relation. In my experience you need at least every 10 fs or

so.

-Dan

*> 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
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*> > 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
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*> > 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
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*> > >
*

*> > > 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
*

*> >
*

*>
*

*>
*

*> --
*

*> ************************************************
*

*> 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>
*

*> ************************************************
*

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Received on Fri Dec 21 2018 - 12:30:02 PST

Date: Fri, 21 Dec 2018 15:04:39 -0500

On Thu, Dec 20, 2018 at 8:14 AM Tom Kurtzman <simpleliquid.gmail.com> wrote:

Brief note here: due to the fact that the velocity autocorrelation

function decays pretty rapidly you have to save velocity information

more frequently than you coordinate information when using the

Einstein relation. In my experience you need at least every 10 fs or

so.

-Dan

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Received on Fri Dec 21 2018 - 12:30:02 PST

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