RE: restraining bonds

From: Tristan Croll (
Date: Mon Sep 01 2014 - 00:57:28 CDT

Yes – see Also, look in VMD at the ssrestraints, chirality restrain and cispeptide restrain plugins. All of these generate extrabonds files for NAMD.

Alternatively, reading your question again I wonder if the RMSD colvar functionality (which will restrain a group of atoms to a set RMSD from a reference structure without preventing bulk movement) is what you’re looking for?

From: Neelanjana Sengupta []
Sent: Monday, 1 September 2014 3:54 PM
To: Tristan Croll
Subject: Re: namd-l: restraining bonds

Dear Tristan,
Can you please be a bit more descriptive? Is this an option in NAMD?

On Mon, Sep 1, 2014 at 11:15 AM, Tristan Croll <<>> wrote:
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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