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

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed May 23 2007 - 13:35:46 CDT

I agree. What I meant was that some people fear of getting the wrong
results if the nonbonded energies are computed with longer steps by
using a MTS scheme. But again, I'm just writing down what others have
shared with me when it comes to these issues.

2007/5/23, Himanshu Khandelia <hkhandel_at_memphys.sdu.dk>:
> 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
> > > -----------------------------
> > >
> > >
> > >
> >
>

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