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

From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Thu May 24 2007 - 10:42:30 CDT

Here's my two cents about this issue,

There's a physical reason why people shy away from SHAKE, in particular when very interested in getting accurate dynamics: slow and fast vibrational modes "talk" to each other, and fast modes may influence slow modes. See Baysal, C., et al., Molecular dynamics analysis of coupling between librational motions and isomeric jumps in chain molecules. Macromolecules, 1996. 29(7): p. 2510-2514.

Getting rid of fast modes by using SHAKE can thus have unexpected outcomes in a simulation. So, I'd be comfortable using SHAKE for Equilibration in most situations, but I'd evaluate carefully whether the 15-20% gains in simulation time are worth the extra uncertainty for actual runs. Normally, whether I use SHAKE or not depends on the problem I'm studying. If I do use SHAKE, I normally run a comparison simulation without it and compare the results to make sure no significant differences occur. Most of the time, however, I find the extra hassle of running that comparison simulation to be a big pain and not worth it for a 15% gain, so I just don't use SHAKE...

I hope this helps,

Ana

_________________________________
Ana CÚlia Ara˙jo Vila Verde
Penn State University
Department of Chemical Engineering
Fenske Laboratory
University Park, PA 16802
USA
 
 
Phone: +(1) (814) 863-2879
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_________________________________

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Himanshu Khandelia
Sent: Thursday, May 24, 2007 9:47 AM
To: Gianluca Interlandi
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Why is SHAKE not being used in typical NAMD simulations ?

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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