Re: SHAKE Tolerance and Performance

From: Nicholas M Glykos (
Date: Thu Mar 01 2012 - 03:16:05 CST

Hi Aron,

> At some point, in playing around with something for a particular system, I
> discovered that in AMBER when one uses SHAKE and a 2fs timestep, you get
> pretty close to a 100% boost in performance. In NAMD, you generally get
> something in range of 15-30%, and since I'd been doing most of my work with
> SHAKE, that seemed to explain the difference.

I believe that most people leave the default for 'useSettle' (which is on)
and, thus, use SETTLE for waters. The implication is that for most
applications the performance difference by changing the tolerance will be
much lower than the 70% you implied (I did a quick check with a node
equipped with a GTX295 card and the difference was only ~3% faster with a
tolerance of 1.0e-5).

My twocents,

            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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