Hi, Sorry to pull a self-publicity plug, but you could use our MDDriver library [1] to implement whatever constraint you want as long as it can be calculated from the system positions and translates into forces to be applied to your system. Such a 'scripting' application is very briefly hinted at in the corresponding paper [2].
Cheers, Marc [1] http://www.baaden.ibpc.fr/projects/mddriver/ [2] http://dx.doi.org/10.1002/jcc.21235 >>> David van der Spoel said: >> Sam Moors wrote: >> > Hi, >> > >> > Position restraints do not allow me to do what I want. >> > For instance, I want to allow the system to freely explore the >> > conformational space within a certain RMSD range, but not evolve beyond >> > a specified RMSD cutoff. >> > Another application would be to push the system conformation away from >> > the reference structure, by using negative force constants. >> > Therefore the reference structure should be fitted to the simulation >> > structure (or the other way around) before calculating the position >> > differences. >> >> Then you have to derive a force that is the derivative of the RMSD with >> respect to the positions. This may be difficult, since you have the >> superposition step in between. What you could do straight away is move >> from normal RMSD to distance-based RMSD, in which case the this has been >> implemented using distance restraints. You would use genrestr to >> generate the additional topology input, then determine a suitable force >> constant and Bob's your uncle. >> >> Cheers. >> > >> > Thanks in advance for your help, >> > Sam >> > >> >> >> >> Mark Abraham wrote: >> >>> Sam Moors wrote: >> >>>> Hi gmx users/developers, >> >>>> >> >>>> I would like to do a molecular dynamics simulation with a restraint on >> >>>> the backbone RMS deviation from a reference structure. >> >>>> Does anybody know if this is possible? >> >> >> >> How about position restraints only on the backbone? Same effect. >> >> >> >>> >> >>> Not exactly as you describe, but you should read the section in chapter >> >>> 4 of the manual and see for yourself. >> >>> >> >>>> If yes, could you explain how to do it? >> >>>> If no, what would be the easiest way to implement this in gromacs? >> >>> >> >>> It could be done, but I'm not sure it's worth the effort. >> >>> >> >>> Mark >> >>> _______________________________________________ >> >>> gmx-users mailing list gmx-users@gromacs.org >> >>> http://www.gromacs.org/mailman/listinfo/gmx-users >> >>> Please search the archive at http://www.gromacs.org/search before >> >>> posting! >> >>> Please don't post (un)subscribe requests to the list. Use the www >> >>> interface or send it to gmx-users-requ...@gromacs.org. >> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> >> -- >> >> David van der Spoel, Ph.D., Professor of Biology >> >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. >> >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. >> >> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> >> >> >> >> >> ------------------------------ >> >> >> >> _______________________________________________ >> >> gmx-users mailing list >> >> gmx-users@gromacs.org >> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> >> Please search the archive at http://www.gromacs.org/search before >> >> posting! >> >> >> >> End of gmx-users Digest, Vol 61, Issue 77 >> >> ***************************************** >> >> >> > _______________________________________________ >> > gmx-users mailing list gmx-users@gromacs.org >> > http://www.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at http://www.gromacs.org/search before posting ! >> > Please don't post (un)subscribe requests to the list. Use the www >> > interface or send it to gmx-users-requ...@gromacs.org. >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. >> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php