To be honest I'm not entirely sure about that either, as the subtleties of
that relation is beyond my expertise. My preferred method is to integrate
the velocity autocorrelation function, as I'm slightly more comfortable
with the Green-Kubo relations and the similarities to calculating
statistical inefficiency. The results should, in principle, be the same,
although I expect that the two approaches are only rarely in perfect
agreement.
Brian
On Thu, Sep 20, 2012 at 3:49 PM, Mo Chen <mc842.cornell.edu> wrote:
> Hi Brian,
> Thank you for the discussion! Yes, by "tau", I meant the lag time. I agree
> with the ensemble part, though with respect to "MSD vs. lag time plot
> should only be linear in the long time limit", I am not quit sure about
> this. I though at least for water, we are always expecting the whole range
> to be linear.
>
> Thanks,
> Mo
>
> On Thu, Sep 20, 2012 at 2:06 PM, Brian Radak <radak004.umn.edu> wrote:
>
> > Mo,
> >
> > I'm not quite sure what you mean by "tau," is this the lag time between
> > frames? The MSD vs lag time plot should only be linear in the long time
> > limit (although it may appear linear throughout). In retrospect I suppose
> > that the stochastic nature of Langevin dynamics means that this type of
> > relation may not hold, even in this limit. My initial thought was that
> > there would be well defined diffusion (although not in terms of physical
> > time) and that it would be impacted by the collision parameter (which I
> > believe can actually be related to the diffusion coefficient of the
> solvent
> > if desired). Anyway, that is all pure speculation on my part.
> >
> > To answer the probably more important question here, yes, if you want a
> > diffusion coefficient that is physically meaningful in the sense that it
> > corresponds to "real" time then you need to run NVE dynamics. However,
> the
> > averages in this case are over the canonically distributed *initial
> > conditions,* not the microcanonical ensemble of configurations generated
> by
> > the dynamics (if the NVE dynamics are ergodic then all initial
> > configurations give equivalent, time reversible trajectories in the long
> > time limit).* *That is, NVE dynamics preserves the canonical weight
> (since
> > energy is conserved) and thus any single NVE run is only one part of the
> > average. Of course, if you take one NVE trajectory with the highest
> > canonical weight it will contribute the biggest part of the average and
> you
> > are done. That's just basic ensemble equivalence. I digress.
> >
> > In my opinion, what you need is a long NVT trajectory (such your Langevin
> > dynamics trajectory) to be assured that you have a converged ensemble of
> > initial conditions and then perform multiple NVE trajectories from
> multiple
> > initial conditions. Taking the MSD vs time plot from that ensemble of
> > trajectories should give you the information you want.
> >
> > Regards,
> > Brian
> >
> >
> > On Thu, Sep 20, 2012 at 1:17 PM, Mo Chen <mc842.cornell.edu> wrote:
> >
> > > Hi Brian,
> > > I have run the NVT Langevin dynamics for hundreds of nanoseconds, but
> the
> > > MSD vs. tau curve of the organic ions was not linear. I understand now
> > that
> > > the the self-diffusion coefficient calculated from a Lagenvin dynamics
> > > simulation is not physically meaningful. As you said, the diffusion
> could
> > > be well defined. So I wonder if I should definitely redo my simulation
> > > using NVE simulation (ntt=0) to get meaningful self-diffusion
> > coefficient?
> > > Or calculation-wise, the self-diffusion coefficient should not be much
> > > different between the two calculations. Thank you!
> > >
> > > Best,
> > > Mo
> > >
> > > On Thu, Sep 20, 2012 at 1:03 PM, Brian Radak <radak004.umn.edu> wrote:
> > >
> > > > What kind of problem are you looking for? I believe Professor Case's
> > > point
> > > > was that diffusion calculated from a Langevin dynamics simulation is
> > not
> > > > physically meaningful, but it is probably well defined and calculable
> > so
> > > > long as you do not perform wrapping.
> > > >
> > > > Regards,
> > > > Brian
> > > >
> > > > On Thu, Sep 20, 2012 at 12:40 PM, Mo Chen <mc842.cornell.edu> wrote:
> > > >
> > > > > Hi David,
> > > > > Sorry, actually I was running NVT simulations actually.
> > > > >
> > > > > Best,
> > > > > Mo
> > > > >
> > > > > On Thu, Sep 20, 2012 at 12:10 PM, Mo Chen <mc842.cornell.edu>
> wrote:
> > > > >
> > > > > > Hi David,
> > > > > > I have run NVE simulations for the system. Below is my input
> file.
> > > May
> > > > I
> > > > > > ask if you think there is still a problem? Thank you!
> > > > > >
> > > > > > Sample pulling input
> > > > > > &cntrl
> > > > > > nstlim=10000000, cut=12.0,
> > > > > > ntpr=1000, ntwx=1000, ntt=3, gamma_ln=1.0,
> > > > > > imin=0, ntx=7, irest=1, ig = -1,
> > > > > > ntb=1, ntc=2, ntf=2, tol=0.00001,
> > > > > > dt=0.002, tempi=363., temp0=363.
> > > > > > /
> > > > > > &ewald vdwmeth=0 /
> > > > > > /
> > > > > > END
> > > > > > eof
> > > > > >
> > > > > >
> > > > > >
> > > > > > Best,
> > > > > > Mo
> > > > > >
> > > > > > On Thu, Sep 20, 2012 at 8:56 AM, David A Case <
> > > > case.biomaps.rutgers.edu
> > > > > >wrote:
> > > > > >
> > > > > >> On Tue, Sep 18, 2012, Mo Chen wrote:
> > > > > >>
> > > > > >> > I am running Langevin dynamics simulations (ntt=3) for organic
> > > > solvent
> > > > > >> > using Amber 11, and would like to calculate the self-diffusion
> > > > > >> coefficient
> > > > > >>
> > > > > >> Just a note: diffusion properties will be messed up by the use
> of
> > > > > (almost
> > > > > >> any) thermostat. So you should not expect the results to be
> > > > physically
> > > > > >> meaningful. If you want to study dynamics, you need to run NVE
> > > > > >> simulations.
> > > > > >>
> > > > > >> ...dac
> > > > > >>
> > > > > >>
> > > > > >> _______________________________________________
> > > > > >> 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
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > ================================ Current Address
> > =======================
> > > > Brian Radak :
> BioMaPS
> > > > Institute for Quantitative Biology
> > > > PhD candidate - York Research Group : Rutgers, The State
> > > > University of New Jersey
> > > > University of Minnesota - Twin Cities : Center for
> > > Integrative
> > > > Proteomics Room 308
> > > > Graduate Program in Chemical Physics : 174 Frelinghuysen
> Road,
> > > > Department of Chemistry : Piscataway,
> NJ
> > > > 08854-8066
> > > > radak004.umn.edu :
> > > > radakb.biomaps.rutgers.edu
> > > > ====================================================================
> > > > Sorry for the multiple e-mail addresses, just use the institute
> > > appropriate
> > > > address.
> > > > _______________________________________________
> > > > AMBER mailing list
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > 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
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Thu Sep 20 2012 - 13:30:04 PDT
