From: Edelmiro Moman (moman_at_titus.u-strasbg.fr)
Date: Tue Jun 20 2006 - 10:20:09 CDT
Hello,
I do not know a work of Tcl scripting (or almost any other scripting
language). In consequence, when I try to use a modified version of the
NAMD sample.conf file, I get all kind of warning messages (if I use
constraints, they tell me about bad geometries; otherwise they complain
about high velocities) and the simulation is immediately aborted. I
(ignorant) suspect that NAMD is starting directly with the MD simulation
without doing a previous minimization (as I would wish). This is the
relevant (I guess) fragment of the file:
______________________________________________________________
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
if {0} {
minimize 100
reinitvels $temperature
}
run 50000 ;# 100ps
______________________________________________________________
First silly question: Am I right (by chance)?
Second silly question: What can I do?
Some clues: If the system has been previously minimized the simulation
uses to runs uneventfully; but (!) Autopsfgen removes the hydrogens from
my system and add them again, as a result of which the geometry of the
prolines uses to be completely wrong and that takes me to the original
problem.
Kind regards,
Miro
P.S.: I am not as lazy as I am ignorant. However, as I am aware that my
messages can hurt certain sensibilities, I have include a warning in the
subject so that sensitive people do not have to read them. About
unnecessarily increasing network traffic, I am very sorry about that and
I plan to punish myself as soon as I can think of a suitable way of
doing it.
-- Edelmiro Moman Institut de génétique et de biologie moléculaire et cellulaire Laboratoire de biologie et de génomique structurales 1, rue Laurent Fries F-67404 Illkirch Cedex FRANCE Tél. : +33 (0)3 88 65 3309 or 3310 Fax : +33 (0)3 88 65 32 76 momanATigbmcDOTu-strasbgDOTfr
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