Spherical restraints

From: Almeida-HernŠndez, 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
Universitštsstr. 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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