RE: restraining bonds

From: Tristan Croll (
Date: Mon Sep 01 2014 - 00:45:22 CDT

Why not just use extrabonds?

From: [] On Behalf Of Neelanjana Sengupta
Sent: Monday, 1 September 2014 2:50 PM
Subject: namd-l: restraining bonds

Dear NAMD community,
I need to do a protein simulation, wherein all individual bonds between the non-hydrogen atoms are harmonically restrained. (I do not wish to restrict the overall translation of the protein). Since there are many such bonds, the colvar option "distance" (with group1 and group2) may not work.
Any suggestions on how to go about this?
Thanks in advance.

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