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 <[email protected]> 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:* "[email protected]" <[email protected]> >> *To:* [email protected] >> *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 <[email protected] <mailto:[email protected]>>: >> >> > 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 >>> >> > --gmx-users mailing list [email protected] <mailto: >> [email protected]> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> >> > Please search the archive at >> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> >> > Please don't post (un)subscribe requests to the list. Use the www >> > interface or send it to [email protected] <mailto: >> [email protected]>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> gmx-users mailing list [email protected] <mailto: >> [email protected]> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected] <mailto: >> [email protected]>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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