AW: restraining

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Aug 24 2012 - 01:42:27 CDT

Hi,

also, as far as I know, the H-O-H in TIP3P is not rigid because of the bond,
but because the angle is fixed by default. The SHAKE is, as I think, only
applied for the O-H bonds. So you can't use SHAKE for that. But you could
just try to introduce a fixed angle. Therefore you could modify the
forcefield of your molecule itself by using a high force for the angle for
example, or use the NAMD feature extrabonds which also allows to introduce
extra angles to the system with a custom force.

It would also be interesting which force field you are using.

regards

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Chris Harrison
> Gesendet: Freitag, 24. August 2012 05:30
> An: cnrowley_at_mun.ca
> Cc: namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: restraining
>
> Two possibilities:
>
> 1) You should be able to effectively accomplish this by imposing an
> extremely high force constant in either the "restraints/constraints"
> or the "colvars" approach.
>
> 2) To utilize the SHAKE algorithm directly in such a manner, ......
> does your topology/PSF file include an explicit H-H bond for HS?
>
> Chris
>
>
> On Thu, Aug 23, 2012 at 10:20 PM, Christopher Rowley
> <cnrowley_at_gmail.com> wrote:
> > Sorry, I should have been more clear about this: I want to keep the
> hydrogen
> > sulfide molecules rigid according to the equations by imposing the
> SHAKE
> > algorithm on the H-H distance, like in rigid water molecules.
> >
> > Thanks,
> > Chris
> >
> >
> > On 24/08/2012 12:38 AM, Chris Harrison wrote:
> >>
> >> '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
> >>>
> >>>
> http://www.mun.ca/cc/policies/electronic_communications_disclaimer_2012
> .php
> >>>
> >>
> >>
> >
>
>
>
> --
> 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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