Re: restraining

From: Christopher Rowley (cnrowley_at_gmail.com)
Date: Thu Aug 23 2012 - 22:20:55 CDT

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
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>>
>
>

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