On 29/12/2010 7:44 AM, Justin A. Lemkul wrote:
TJ Mustard wrote:
Hi,
I am trying to speed up my parallel processor Gromacs jobs and was
wondering what were the known settings for PME cut-off and PME grid
spacing? As of now I am running with a PME cutoff of 0.8 and a
fourierspacing of 0.12.
There are a great many factors that contribute to the speed and accuracy
of the GROMACS PME implementation. However, if you've used the default
ewald_rtol of 1e-5, then I think your rcoulomb is much too small.
What do you mean by "known settings"? The cutoff (rcoulomb) can be
dictated by the force field used, although with PME I think the
results are relatively insensitive to small changes. The grid spacing
affects accuracy - larger spacing implies less grid points and faster
speed, but lower accuracy. I do not know if there has been any
systematic investigation into these effects, though.
There hasn't been an investigation of the influence of PME accuracy on
simulation results. I have a manuscript that should be in press shortly,
which deals with many of the considerations in choosing these
parameters. In it, I observed that "typical" GROMACS parameters values
of rcoulomb=1.0, fourierspacing=0.10 and ewald_rtol=1e-5 in 4.5.3 led to
a relative RMS error in the electrostatic forces around 2e-4. That error
was well balanced between real and reciprocal space, but with 24 PME
nodes out of 64, the PME nodes did 8.1% too much work. The problem is
that we don't know whether this is sufficiently accurate for any purpose.
Mark
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