Dear Justin, Thanks for your reply.. But I am not getting how and where should I give the option of energy_excl. For freezing a part of molecule ? what are the other checks to be done for the same ?
With Thanks, Vivek 2008/10/14 Justin A. Lemkul <[EMAIL PROTECTED]> > > > vivek sharma wrote: > >> >> >> 2008/10/14 Justin A. Lemkul <[EMAIL PROTECTED] <mailto:[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 ? >> >> > I've never used freezegrps for any large set of atoms, so maybe. If you've > got surrounding solvent, though, the nonbonded interactions are still > calculated between the frozen group and solvent, unless you turn that off > too. But then it starts getting really unphysical, in my view. > > -Justin > > Thanks, >> ~Vivek >> >> >> >> -Justin >> >> With Thanks, >> Vivek >> >> 2008/10/12 Erik Lindahl <[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]> <mailto:[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> >> <mailto: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/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use thewww >> interface or send it to [EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]> >> <mailto:[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 >> <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 the >> www interface or send it to [EMAIL PROTECTED] >> <mailto:[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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> 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 the www >> interface or send it to [EMAIL PROTECTED] >> <mailto:[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 > > ======================================== >
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