Hi there, I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot for the same), thanks for your suggestions regarding the same. But, I have seen that the part of the molecule I kept for PR is still having some motion, how can I keep that part rigid ? I am not getting any idea of energy_excl option mentioned above, please explain.
With Thanks, Vivek 2008/10/12 Erik Lindahl <[EMAIL PROTECTED]> > Hi, > > On Oct 10, 2008, at 12:46 PM, Justin A. Lemkul wrote: > >> >>> I want to run MD over a part of my molecule , for few residues only (not >>> the whole molecule). >>> Can I do it using GROMACS ? >>> I searched for the online documentation and mailing list, but unable to >>> get appropriate information. >>> If somebody has already tried such things earlier, please suggest and >>> direct me for appropriate link and address. >>> >> >> Well, if your goal is to keep certain parts fixed and allow others to >> move, probably the easiest way to do it is to apply position restraints to >> the "fixed" part. >> > > You can also set parts of the system as a freeze group, in which case you > can exclude all nonbonded interactions inside the freeze group with the > energygrp_excl option in your mdp file. > > The main advantage of this is of course that you will improve performance > if 99% of your system is frozen (although all interactions between the > frozen and non-frozen parts still have to be calculated). On the other hand, > completely freezing part of the system is not very realistic, and you're > likely to get strange behavior in the interface... > > Cheers, > > Erik > _______________________________________________ > 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 thewww interface > or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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