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

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed May 23 2007 - 18:05:18 CDT

There have been already discussions in the NAMD list about the use of
different timesteps. In particular, it seems that the use of a multi
stepping algorithm seems to cause an energy drift:

http://www.ks.uiuc.edu/~sotomayo/private/answer.html

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5385.html

Usually, the conservation of energy is used as a "quality control" for the
algorithm and timestep used. Thus if you are concerned about whether the
chosen timestep is good or not the first thing to do would be to check
whether the energy and temperature are conserved.

Gianluca

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

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

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                    +1 (206) 714 4303
                    http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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