From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 24 2012 - 03:09:54 CDT
On Fri, Aug 24, 2012 at 8:42 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
> 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
correct. the H-H bond is used in CHARMM and Amber to make water
molecules rigid through a 3 bond constraint. NAMD will ignore this, since
i has code that recognizes water molecules based on some heuristics.
> 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.
the better solution would be to modify the NAMD source code to recognize
the H2S as a water and then use the special optimized code for computing
rigid water molecules. it would be *much* more efficient.
cheers,
axel.
>
> 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
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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