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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> 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
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Received on Thu Sep 20 2012 - 10:30:02 PDT
