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
colvars
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>
Hello:
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
charges.
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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