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

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Wed May 23 2007 - 13:30:11 CDT

It is common practice to use SHAKE without MTS in most simulation programs
(CHARMM, GROMACS, AMBER). So reliability should not be an issue

On Wed, 23 May 2007, L. Michel Espinoza-Fonseca 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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