From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Aug 23 2012 - 22:08:49 CDT
'rigidbonds all' only refers to hydrogen bonds. It is a parameter for
the Rattle/Settle algorithm.
You are looking for either "restraints/constraints":
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html#5771
or the "colvars module":
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node53.html
Either option should allow you to set the restraints you describe.
Chris
On Thu, Aug 23, 2012 at 1:55 PM, Christopher Rowley <cnrowley_at_mun.ca> wrote:
> 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
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>
-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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