Why is SHAKE not being used in typical NAMD simulations ?

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Wed May 23 2007 - 08:06:04 CDT


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

Thank you for the help,


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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