From: Almeida-Hernández, Yasser, Dr. (yasser.almeida-hernandez_at_uni-due.de)
Date: Tue Apr 06 2021 - 09:07:44 CDT
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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