From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Mar 11 2015 - 12:28:44 CDT
To the extent that it is worth telling (and reading), the problem was
solved by running the system (solvated/salted in a periodic box) with more
cores and two GTX680.
Previously, as the protein is rather small, I used for minimizing the
desktop with large memory but two fast cores only.
fp
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Mar 11, 2015 at 12:38 PM
Subject: namd-l: No steric clashes, still not minimizing
To: NAMD <namd-l_at_ks.uiuc.edu>
Hallo:
Minimization of the non solvated system under GB conditions runs fine. In
contrast, the TIP3 solvated/ion-added system resists
minimization/velocityQuenching .
No indication of clashes:
lsort -unique -increasing -integer [join [measure contacts 1.4 [atomselect
top "noh"]]]
>Main< (psfgen) 36 %
It is only at 1.5A that the above command reveals a two atoms.
However, at
timestep 0.000001
maximumMove 0.000001
with
rigidBonds water
rigidTolerance 0.000001
exclude scaled1-4
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5 # cutoff +3.5
margin 5
1-4scaling 1.0
error arises:
TCL: Running for 1000 steps
FATAL ERROR: Low global exclusion count! (97807 vs 97818) System unstable
or pairlistdist or cutoff too small.
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Low global exclusion count! (97807 vs 97818) System
unstable or pairlistdist or cutoff too small.
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
Charm++ fatal error:
FATAL ERROR: Low global exclusion count! (97807 vs 97818) System unstable
or pairlistdist or cutoff too small.
Thanks for suggestions
francesco Pietra
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