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
> > > >>
> > > >
> > > >
> > > _______________________________________________
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> > >
> >
> >
> >
> > --
> > ================================ 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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--
================================ 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 - 11:30:03 PDT
