<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>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></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> "gyorgy.hantal@fc.up.pt" <gyorgy.hantal@fc.up.pt><br><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span style="font-weight: bold;">Sent:</span></b> Thu, April 7, 2011 6:50:37 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Is
there still interest in rigid-body simulation?<br></font><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>Quoting ms <<a ymailto="mailto:devicerandom@gmail.com" href="mailto:devicerandom@gmail.com">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 that: (a) I am modifying GROMACS 4.5.1, so I am some months out of date,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><span>> <a target="_blank" href="http://devicerandom.org">http://devicerandom.org</a></span><br>> --gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><span>> <a target="_blank"
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