RE: harmonic restraints between multiple atom pairs

From: Tristan Croll (
Date: Mon Nov 03 2014 - 23:20:09 CST

I suspect you’d be better off doing this via NAMD’s extrabonds functionality rather than colvars.

From: [] On Behalf Of Neelanjana Sengupta
Sent: Tuesday, 4 November 2014 2:43 PM
Subject: namd-l: harmonic restraints between multiple atom pairs

Dear All,
I would like to apply harmonic restraints between multiple pairs of atoms in a complex system I am simulating. The force constant applied between each pair is the same.
Is there an efficient way to specify this within the colvars module? (The messy way would be to specify each atom pair, but if I have a fairly large number of pairs, this would be tacky..).
Thanks in advance.

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