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

[Justin A. Lemkul]

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 that: (a) I am modifying GROMACS 4.5.1, so I am some months out of date,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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