From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Jun 20 2006 - 10:38:17 CDT
0 is equivalent to false, so the if { } statement is not executed. You need
to change it to 1. So you are right.
Could you include all the lines you use to generate the psf?
As for the rest of your message, :).
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Edelmiro Moman
Sent: Tuesday, June 20, 2006 10:20 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Tcl, minimization and MD (Warning: I am a lazy ignorant)
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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