From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Aug 23 2012 - 22:29:54 CDT
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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