Hi Justin,<div>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,</div>
<div><br></div><div>Adam<br><br><div class="gmail_quote">On Thu, Apr 7, 2011 at 12:58 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
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:<br>
<br>
1. Post this proposal as a project/enhancement request on <a href="http://redmine.gromacs.org" target="_blank">redmine.gromacs.org</a> (and then volunteer to work on it)<br>
2. Post the idea, framework, time needed, etc to the gmx-developers list so you're reaching a target audience for such tasks<br>
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)<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
Semen Esilevsky wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
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!<br>
<br>
Regards,<br>
Semen<br>
<br>
------------------------------------------------------------------------<br>
*From:* "<a href="mailto:gyorgy.hantal@fc.up.pt" target="_blank">gyorgy.hantal@fc.up.pt</a>" <<a href="mailto:gyorgy.hantal@fc.up.pt" target="_blank">gyorgy.hantal@fc.up.pt</a>><br>
*To:* <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
*Sent:* Thu, April 7, 2011 6:50:37 PM<br>
*Subject:* Re: [gmx-users] Is there still interest in rigid-body simulation?<br>
<br>
<br>
Hello,<br>
<br>
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.<br>
<br>
Thanks in advance.<br>
Best,<br>
<br>
Gyorgy<br>
<br></div><div class="im">
Quoting ms <<a href="mailto:devicerandom@gmail.com" target="_blank">devicerandom@gmail.com</a> <mailto:<a href="mailto:devicerandom@gmail.com" target="_blank">devicerandom@gmail.com</a>>>:<br>
<br>
> On 27/03/11 23:02, Adam Herbst wrote:<br>
>> Hi all,<br>
>> I have seen a few posts on gmx-users indicating a desire to treat<br>
>> certain atom groups as rigid bodies in MD simulations. I just started<br>
>> implementing this, and so far I have it working for translational forces<br>
>> (not rotation, though this should be simple to add), even when the group<br>
>> is split over multiple processors. At the moment I have the rigid body<br>
>> groups specified as freeze groups in the mdp file, but there could be a<br>
>> separate option. Would anyone else find this useful? The problem is<br>
>> that: (a) I am modifying GROMACS 4.5.1, so I am some months out of date,<br>
>> and (b) my code is probably not to spec. If it is worthwhile, I can<br>
>> restart from 4.5.4 (the code modifications are quite small) and make an<br>
>> effort to conform to coding standard. Best,<br>
>><br>
>> Adam Herbst<br>
>><br>
><br>
> I would love that!!<br>
><br>
> --Massimo Sandal, Ph.D.<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<a href="http://devicerandom.org" target="_blank">http://devicerandom.org</a><br>
</blockquote></div>
> --gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im">
<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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