From: Christopher Rowley (
Date: Thu Aug 23 2012 - 13:55:59 CDT


I'm using NAMD for simulations of a model for hydrogen sulphide (H2S).
The model is defined as being rigid, like TIP3P, so I've included the
command "rigidbonds all" Nevertheless, the H-S-H bond is flexible in MD

The PSF file contains a bond between the two hydrogens, but this doesn't
seem to make a difference.

Unless I've misunderstood, H-H bonds should be identified in Molecule.C

           if ( ! is_water(a2) ) { // H-H but not water
             rigidBondLengths[a1] = ( mode == RIGID_ALL ? x0 : 0. );
             rigidBondLengths[a2] = ( mode == RIGID_ALL ? x0 : 0. );

Is there a way to force NAMD to constrain this distance/angke?


Christopher Rowley
Ph.D. (chemistry)
Assistant Professor
Department of Chemistry
Memorial University of Newfoundland
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