On 30/12/2010 1:58 AM, Florian Dommert wrote:
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On 12/29/2010 12:56 AM, Mark Abraham wrote:
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
You can estimate the error of SPME with the tool g_pme_error and also
determine the optimal ewald_rtol to distribute the error equally over
real and fourier space. As Justin mention the real space cutoff is often
given by the force field
To my knowledge, the only (GROMACS) force field that was parameterized
with PME in mind is AMBER03, and IIRC that paper does not fully describe
the PME regime used during parameterization. So, while all the
forcefields had a real-space cut-off, it was for a different
electrostatics model. Thus, so long as the PME error is at worst
comparable to that introduced by the parametrization method, there is no
reason why rcoulomb cannot be varied from the parameterization value.
Caveat: since rcoulomb == rvdw, for a given ewald_rtol, you don't want
to make rcoulomb so small that the VDW error now dominates the
non-bonded error.
Mark
so you just have to decrease the fourierspacing
and/or the interpolation order to obtain the desired accuracy, but be
aware that the error estimate is just valid for even interpolation
orders. The tool g_tune_pme allows to find the optimal number of PME
nodes and perhaps suggest small changes of the cutoff and/or the
gridspacing. Though the tuning can consume some time you will save much
more time for your production run and g_pme_error is even MPI capable to
speed up the error estimate.
/Flo
- --
Florian Dommert
Dipl.-Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
Phone: +49(0)711/685-6-3613
Fax: +49-(0)711/685-6-3658
EMail: domm...@icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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