2008/10/14 Justin A. Lemkul <[EMAIL PROTECTED]> > > > vivek sharma wrote: > >> 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 ? >> > > Position restraints do not necessarily guarantee that atomic positions stay > absolutely fixed. Instead, there is an energy penalty for moving them, > which could in some cases be overcome. > > I am not getting any idea of energy_excl option mentioned above, please >> explain. >> >> > The freezegrps option can be used to fix atomic positions, but in this case > large forces can be generated within the frozen group. As such, you can > apply energygrp_excl to exclude energetic terms within the frozen group.
Will it help me in reducing the time taken for the simulation if I'll keep the part of molecule frozen ? Thanks, ~Vivek > > > -Justin > > With Thanks, >> Vivek >> >> 2008/10/12 Erik Lindahl <[EMAIL PROTECTED] <mailto:[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 >> <mailto: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] >> <mailto:[EMAIL PROTECTED]>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
_______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php