hi, ok the next question that bugs me is if i make a directory consisting of my modified force field (*.atp, *.rtp, *bon.itp,*nb.itp) and i want to use pdb2gmx to get the *.top & .gro files according to the above new FF files, how do i supply this info to pdb2gmx. In other words how do i make pdb2gmx aware of the new FF files.
Amit On Tue, Sep 8, 2009 at 6:58 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Amit Choubey wrote: > >> Hi, >> >> so is it a good idea to edit the original gromacs files in top directory >> for introducing new force field or is there a way to compliment the existing >> FF files by a new file made by me? >> > > It is generally better to not mess with system-level force field files > unless you're very sure of what you're doing, and experienced in making such > changes. If you alter one of the original force field files, and you don't > do it right, reverting the changes is often difficult. If, for example, you > want to modify the OPLS-AA force field, do not ever make any changes to the > original file, instead implement them in files like ffoplsaa_mod.* > > It is even safer to implement your changes in the local directory until you > are confident everything is working properly, then if you're comfortable > that you've done everything 100% right, move your files into /share/top for > convenience later. > > -Justin > > >> Amit >> >> On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Amit Choubey wrote: >> >> hi gromacs user, >> >> Is there any good way to introduce new force field in the >> gromacs library? >> >> >> Read in the manual about the organization of existing force fields, >> as well as the component files that are necessary to make it >> function. Beyond that, look at the implemented force fields >> themselves and see how they work together. >> >> -Justin >> >> Amit >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> 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://lists.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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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://lists.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 >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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