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 - 11:15:42 CDT

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

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