Fwd: Constraint failure in RATTLE

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Mar 30 2014 - 03:07:50 CDT

I could restart from restart files (including colvars) at where the
simulation crashed. I had preferred to restart from a previous frame, where
I know from VMD how to get the restart files, except about the state of
colvars. Thanks for suggesting how to get the latter.

francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sun, Mar 30, 2014 at 9:31 AM
Subject: namd-l: Constraint failure in RATTLE
To: NAMD <namd-l_at_ks.uiuc.edu>

This is to report a rather unusual "constraint failure in RATTLE algorithm
for atom 520" during non-periodic accelMD under GB conditions with namd2.9.

Atom 520 is CA of a TRP residue that makes part seven residues at one end
of a 37-residue peptide, and which are under rmsd colvars, keeping them as
an alpha-helix stretch.

This accelMD followed a series of similar accelMD, which were started after
a series of T-REMD under either non-periodic GB or periodic explicit
conditions. There was no crash before the one above. Otherwise, folding was
going on smoothly, albeit still far from completion.

Graphics does not suggest any unusual situation for CA 520. Also, namd plot
with the log file shows constant energy, even when magnified.

francesco pietra

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