Re: PME and r-RESPA issue in NAMD

From: Axel Kohlmeyer (
Date: Sat Jun 07 2008 - 09:50:59 CDT

On Sat, 7 Jun 2008, sudipta sinha wrote:

SS> Hi All,
SS> Could anyone suggest me how we determine PMEGridSizeX,
SS> PMEGridSizeY, PMEGridSizeZ in NAMD. Are these values choosen as
SS> boxl/PMEGridSizeX, boxl/PMEGridSizeY, boxl/PMEGridSizeZ are approximately
SS> equal to 1 or less than one and I am curious to know about the integer
SS> factor (2, 3, 5) of grid points. Another thing I want know which combination

please check out the literature on PME. there are bunch of papers (don't
have the references here, but paul crozier mentioned them a while ago
on the lammps mailing list, so you may search their archive)
investigating the accuracy of PME and related methods. using one grid
point per angstrom was found to be reaching a good balance between
real space and k-space calculation at acceptable accuracy and the
fact that the total number of grid points has to be multiples of
2,3,5 is a limitation of fast fourier transforms (in principle FFTW
supports roots up to 13, but the smaller ones are more efficient).

SS> of r-RESPA gives the best performance for parallel running. We are using
SS> timestep=2fs, fullectrostaticfrequency=2, nonbonded=1

r-RESPA is a completely different story. whatever parameters you choose
it is always a compromise between accuracy & energy conservation
and performance. _you_ have to determine what is an acceptable
energy conservation and accuracy and based on that you can choose
the respa parameters to so they stay within those boundaries and
give the best performance. since this tends to be dependent on the
kind of system you are running, you have to make tests by yourself.


SS> Thanks
SS> Sudipta

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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