From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Thu May 24 2007 - 08:46:59 CDT
Please note that this post is not about using multiple time stepping, and
energy drifts. It is about SHAKE. I am hoping some of the developers will
be able to tell us why SHAKE is not recommended in NAMD, while it is in
other programs ?
----------------------------
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
-----------------------------
On Wed, 23 May 2007, Gianluca Interlandi wrote:
> 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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