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

From: Eric Cyr (ericcyr_at_uiuc.edu)
Date: Wed May 23 2007 - 13:20:34 CDT

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
> > -----------------------------
> >
> >
> >
>

-- 
4330 Siebel Center
201 N. Goodwin Ave.
Urbana, IL 61801
http://www.cse.uiuc.edu/~ericcyr/

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:46:20 CST