Re: Constraint bonds that does not include hydrogrens

From: Jeff Comer (
Date: Thu Dec 22 2016 - 09:38:50 CST

Hi Karteek,

NAMD only applies rigid bonds to hydrogen atoms. It decides what is
hydrogen based on mass. If you want to rigidify other bonds, you can
either reduce the atom's mass to something greater than 1.0 and less
than 3.5 or alter the code that decides whether the atom is hydrogen
or not. See the line "} else if (atoms[atom_number-1].mass <=3.5) {"
in Molecule.C. You can change it to something like the following for
to get atoms named "X..." to be identified as hydrogen:

} else if ( atoms[atom_number-1].mass <=3.5 ||
atomNames[atom_number-1].atomname[0] == 'X' )

I've only done this for atoms with a single bond. I'm not sure it
works for other geometries.


Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Wed, Dec 21, 2016 at 11:00 PM, Karteek Bejagam <> wrote:
> Dear NAMD users,
> I would like to constrain a bond that does not involve hydrogen.
> I have tried to use "rigidBonds all" but it fails.
> Can anyone help me to figure out any way to constrain the bond?
> I was looking for algorithms like SHAKE/RATTLE/SETTLE to constrain a bond.
> Thanks in advance,
> Karteek

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