Re: AW: restraining

From: Christopher Rowley (cnrowley_at_mun.ca)
Date: Fri Aug 24 2012 - 08:08:42 CDT

In general, other codes make water molecules rigid by imposing a SHAKE
constraint on the distance between the two hydrogens (AMBER and CHARMM
for sure, I assume the others do too). The SHAKE algorithm is much
easier to apply to a distance than an angle. A three-atom molecule where
the distances between all atoms is constant is rigid, so this is a much
simpler way of achieving a truly rigid molecule.

We are using the Jorgensen hydrogen sulphide model, analogous to to
TIP3P water ( J. Phys. Chem.,1986,90(23), pp 6379--6388).

In any case, it seems inevitable that I will take Axel's suggestion and
modify Molecule.C to recognize these molecules and add a constraint
between their two hydrogens. In general, I would suggest that NAMD
should consider imposing shake on any H-H bond that is defined in the
PSF when rigidbonds all is on. Many small molecule force fields impose
rigidity this way and to be consistent with their parameterization, they
should be strictly rigid.

Thanks,
Chris

On 08/24/2012 04:12 AM, Norman Geist 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
> 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
>

-- 
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

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:25 CST