Fwd: Stray PME grid charges on increasing number of replicas and T-range with T-REMD

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Sep 10 2013 - 05:33:03 CDT

For completeness, and to the extent that it may be relevant, I forgot to
mention that the portion of the peptide well defined under X-ray
diffraction (a couple of alpha helical turns) was restrained with rmsd

 outputSystemForce yes # reports also colvar system force

  rmsd {
     atoms {
       # add all the C-alphas within residues 41 to 48 of segment "P2I"
        psfSegID P2I
       atomNameResidueRange CA 41-48
     refPositionsFile npt-02.pdb ;# renamed from npt-02.coor

# apply harmonic potential to the "rmsd" variable
# with center on zero
# colvars and centers should both be lists, appearing only once in the block

harmonic {

  name P2i_harmonic

  colvars { colvar1 }

  centers 0.0

  forceConstant 100.0

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Sep 10, 2013 at 12:24 PM
Subject: namd-l: Stray PME grid charges on increasing number of replicas
and T-range with T-REMD
To: NAMD <namd-l_at_ks.uiuc.edu>

With debug (64 nodes, 1024 processors) T-remd (parallel tempering), on
increasing the number of replicas, from 16 to 32, and the corresponding
temperature range from 314-320 to 314-338 (expecting a good exchange for T
gaps of 0.8K as it occurred at 314-320) I am noticing stray PME grid

In a first attempt this occurred at step 1590 (out of expected ca 2000), on
a second attempt at step 190 with, of course, all 32 replicas.

Never had a problem with same input data during extensive NPT MD, or 16
replicas, same ts=2fs.

I should say that PMEGridSizeZ differs much from what is advised on the
manual. See below please what was used for both successful MD, 16 replicas,
and 32 replicas:

cellBasisVector1 60.88 0. 0.
cellBasisVector2 0. 92.45 0.
cellBasisVector3 0. 0. 102.99

cellOrigin -12.409886360168457 36.25075912475586 -53.04564666748047
PMEGridSpacing 1.0
PMEGridSizeX 65
PMEGridSizeY 96
PMEGridSizeZ 105

The system is a 34aa in TIP3 water, total number of atoms 55,118.

Thanks for advice.

francesco pietra

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