By the way thank you very much for answering my questions. Amit
On Tue, Sep 8, 2009 at 7:13 PM, Amit Choubey <kgp.a...@gmail.com> wrote: > 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 >> > >
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