Re: Why is SHAKE not being used in typical NAMD simulations ?

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed May 23 2007 - 13:32:25 CDT

Note: I mentioned this thing about being reliable enough because
others have told me that, so I just said what I was told by my
colleagues, and it doesn't represent my own view :).

2007/5/23, Eric Cyr <ericcyr_at_uiuc.edu>:
> What is meant by "not reliable enough"? I can think of a couple
> of things this could mean.
>
> Eric
>
> On 5/23/07, L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu> wrote:
> > I myself have asked this question before. My answer (as before) is no
> > idea. Perhaps some people think that SHAKE and MTS schemes are not
> > reliable enough (at least this is what some colleagues have told me
> > before).
> >
> > Cheers,
> > Michel
> >
> > 2007/5/23, Himanshu Khandelia <hkhandel_at_memphys.sdu.dk>:
> > > Hello,
> > >
> > > Most NAMD papers describe a simulation timestep of 1 fs, no shake, a
> > > nonbondedfreq of 2, and an fullelecfreq. of 4. This is also what is
> > > recommended in most NAMD tutorials.
> > >
> > > However, use of a 2 fs timestep, a value of 1 for both the nonbondedfreq
> > > and fullelecfreq results in 15-25 % faster performance in my tests. I can
> > > provide more details of the tests if desired, but surely these tests must
> > > have already been performed.
> > >
> > > So why is SHAKE/RATTLE and a larger time step not being used for most
> > > simulations?
> > >
> > > Thank you for the help,
> > >
> > > -Himanshu
> > >
> > > ----------------------------
> > > Himanshu Khandelia, PhD
> > > Research Assistant Professor (Postdoc)
> > > MEMPHYS, Center for Membrane Physics: www.memphys.sdu.dk
> > > University of Southern Denmark (SDU)
> > > Odense M 5230, Denmark
> > >
> > > Phone: +4565503510
> > > email: hkhandel_at_memphys.sdu.dk
> > > WWW: www.memphys.sdu.dk/~hkhandel
> > > -----------------------------
> > >
> > >
> > >
> >
>
>
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