From: Christopher Rowley (cnrowley_at_mun.ca)
Date: Thu Aug 23 2012 - 13:55:59 CDT
Hi,
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
simulations.
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
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?
Thanks,
Chris
-- Christopher Rowley Ph.D. (chemistry) Assistant Professor Department of Chemistry Memorial University of Newfoundland http://www.chem.mun.ca/homes/cnrhome/ This electronic communication is governed by the terms and conditions at http://www.mun.ca/cc/policies/electronic_communications_disclaimer_2012.php
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