[gmx-users] Is there still interest in rigid-body simulation?

[Adam Herbst]

Hi Justin,
I added this feature as a new issue under the Gromacs project on Redmine.
 Recently I also added a Git fork with a very rudimentary version of rigid
body code.  Let me know if there is anything specific you think I should
work on.  Thanks a lot,

Adam

On Thu, Apr 7, 2011 at 12:58 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
> It seems like lots of people are in favor of this idea.  Since Gromacs is
> undergoing some MAJOR changes to its underlying code, features, etc in the
> coming months it would be prudent to:
>
> 1. Post this proposal as a project/enhancement request on
> redmine.gromacs.org (and then volunteer to work on it)
> 2. Post the idea, framework, time needed, etc to the gmx-developers list so
> you're reaching a target audience for such tasks
> 3. Coordinate your efforts with the core developers who are currently
> developing a pretty detailed roadmap of future development (much of this can
> be done on the redmine site)
>
> All of these will improve the chances of making useful code contributions
> that can eventually get incorporated into a release, or at least a git
> branch somewhere.
>
> -Justin
>
> Semen Esilevsky wrote:
>
>> This would be very good! I'm working on somewhat similar thing, but I plan
>> to use external library for computing rigid body forces from atom forces. If
>> gromacs will be able to compute rigid body forces itself it will be great!
>>
>> Regards,
>> Semen
>>
>> ------------------------------------------------------------------------
>> *From:* "gyorgy.hantal at fc.up.pt" <gyorgy.hantal at fc.up.pt>
>> *To:* gmx-users at gromacs.org
>> *Sent:* Thu, April 7, 2011 6:50:37 PM
>> *Subject:* Re: [gmx-users] Is there still interest in rigid-body
>> simulation?
>>
>>
>> Hello,
>>
>> I think it would be very good to have this feature in gromacs. In fact
>> I've recently had some problems with constraining some species in my
>> simulations. Finally I've sorted out with shake but your solution seems to
>> me less problematic.
>>
>> Thanks in advance.
>> Best,
>>
>> Gyorgy
>>
>> Quoting ms <devicerandom at gmail.com <mailto:devicerandom at gmail.com>>:
>>
>>  > On 27/03/11 23:02, Adam Herbst wrote:
>>  >> Hi all,
>>  >> I have seen a few posts on gmx-users indicating a desire to treat
>>  >> certain atom groups as rigid bodies in MD simulations.  I just started
>>  >> implementing this, and so far I have it working for translational
>> forces
>>  >> (not rotation, though this should be simple to add), even when the
>> group
>>  >> is split over multiple processors.  At the moment I have the rigid
>> body
>>  >> groups specified as freeze groups in the mdp file, but there could be
>> a
>>  >> separate option.  Would anyone else find this useful?  The problem is
>>  >> that: (a) I am modifying GROMACS 4.5.1, so I am some months out of
>> date,
>>  >> and (b) my code is probably not to spec.  If it is worthwhile, I can
>>  >> restart from 4.5.4 (the code modifications are quite small) and make
>> an
>>  >> effort to conform to coding standard.  Best,
>>  >>
>>  >> Adam Herbst
>>  >>
>>  >
>>  > I would love that!!
>>  >
>>  > --Massimo Sandal, Ph.D.
>>
>>>  http://devicerandom.org
>>>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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