So I am not a PME expert and have never quite fully understood the 2-3-5
prime factorization rule for FFT grids. I will refrain from asking such a
detailed and broad question here. However, it would seem that AMBER (or at
least pmemd) is a bit overzealous in enforcing this rule and can also give
conflicting results on the matter.
Case in point:
I have solvated a small molecule in a 45 A cube (set, but not constructed,
in tleap). If I set nfft1 = nfft2 = nfft3 = 45 then pmemd gives an error
reminding about the 2-3-5 rule *and *that these values must be even. Since
I don't really care what the FFT grid is I then just deleted those lines
and let pmemd choose the grid. However the result in the output is not
isotropic, that is, nfft1 = 48 while nfft2 = nfft3 = 45. So apparently my
original choice is only okay when pmemd makes it for me and the isotropic
nature of the system is ignored. Am I wrong in finding this weird and
unsatisfying? Won't the anisotropic grid in principle cause artifacts in
the dynamics and/or affect rotational invariance, or is this really not a
serious problem compared to all of the other numerical/statistical noise?
Regards,
Brian
P.S. It is probably relevant that I'm using AMBER12 with pmemd.MPI on 8
processors and will eventually switch to sander.MPI to perform QM/MM HREMD.
The system is also charged, so care with the PME calculations is of higher
importance than usual.
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 18 2012 - 07:30:04 PDT
