# Re: [AMBER] Problems calculating self diffusion coefficient of water

From: Lucas Bandeira <bandeiralucas97.gmail.com>
Date: Sat, 22 Dec 2018 11:30:37 -0200

Thank you all for your help.

In the article Saeed have sent me they made 80 simulation of 20 ps, each of
them using a different frame of the NPT file (restart file). So I have to
generate the snapshots using cpptraj and then I run the simulation. My
question is: How can I generate this 80 snapshots and run this 80
simulations in a more practical way? I mean, without specifying every
snapshot that I want in the cpptraj command and running all the simulations
once.

Thank you

Lucas

On Fri, Dec 21, 2018 at 6:05 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:

> 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
> > > 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
> > >
> >
> >
> > --
> > ************************************************
> > 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/amber
>
> _______________________________________________
> 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
Received on Sat Dec 22 2018 - 06:00:02 PST
Custom Search