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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> > AMBER.ambermd.org
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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
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Received on Thu Sep 20 2012 - 10:30:03 PDT
