Hi, You can also use essential dynamics sampling. Ran. David van der Spoel wrote: > 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
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