From: Almeida-Hernández, Yasser, Dr. (yasser.almeida-hernandez_at_uni-due.de)
Date: Tue Apr 06 2021 - 10:50:11 CDT
Hi Giacomo,
Thank you for your reply. Yes, that was the problem.
The setting looks now like:
set config "
colvar {
name LIG_sphere
distance {
group1 {atomNumbers 704} # Cu2+ cation
group2 {atomNumbersRange 707-734} # Ligand
}
}
harmonicWalls {
colvars LIG_sphere
outputEnergy on
lowerWalls 0
upperWalls 15
forceConstant 1000
}
"
colvars on
cv config ${config}
Now, if I run it in my laptop it works well, but if I run it in a cluster with GPU (namd2 +idlepoll +isomalloc_sync +p46 +devices 0,1 $INP.conf > $INP.log), it writes -nan values:
TIMING: 89000 CPU: 686.545, 0.0172745/step Wall: 737.674, 0.0173574/step, 4.39239 hours remaining, 672.355469 MB of memory in use.
ENERGY: 89000 nan 888064.2004 nan nan nan 0.0000 0.0000 0.0000 nan nan nan nan -nan nan nan nan nan nan nan
Any thoughts?
Best
________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Tuesday, April 6, 2021 5:06:58 PM
To: NAMD list; Almeida-Hernández, Yasser, Dr.
Subject: Re: namd-l: Spherical restraints
Hello Yasser, there are a few things to check, but the first one would be to make sure that you actually loaded that configuration. There will be a (fairly verbose) set of messages printed when you do.
What you did there is setting a string variable "config" to contain the configuration text, which can be used in a Tcl script but you actually need to load it afterwards, e.g.:
cv config ${config}
On Tue, Apr 6, 2021 at 10:09 AM Almeida-Hernández, Yasser, Dr. <yasser.almeida-hernandez_at_uni-due.de<mailto:yasser.almeida-hernandez_at_uni-due.de>> wrote:
Hello,
I want to spherically restrain a ligand around a Cu2+ cation with harmonic walls. For this, I am using the colvars module as:
# Restraint the ligand in a sphere of r=15 AA around the Cu2+
set config "
colvars on
colvar {
name LIG_sphere
distance {
group1 {atomNumbers 704} # Cu2+ cation
group2 {atomNumbersRange 707-734} # Ligand
}
}
harmonicWalls {
name LIG_sphere
colvars HL
outputEnergy on
lowerWalls 0
upperWalls 15
forceConstant 1000
}
"
.. but it doesn't work. The ligand tumbles all around.
Am I missing something? Any help will be appreciated.
Best,
Yasser
-- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T01 R03 D45 Faculty of Biology University of Duisburg-Essen Universitätsstr. 2, 45117 Essen Email: yasser.almeida-hernandez_at_uni-due.de<mailto:%20yasser.almeida-hernandez_at_uni-due.de> Phone: +49 201 183 2457<tel:+49%20201%20183%202457>
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