On Wed, Jun 19, 2013 at 9:41 AM, Steven Neumann <s.neuman...@gmail.com> wrote: > On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > >> On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann <s.neuman...@gmail.com >> >wrote: >> >> > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> > >> > > >> > > >> > > On 6/10/13 5:16 AM, Steven Neumann wrote: >> > > >> > >> Thank you. >> > >> Do you know whether it is possible to use the 5th order polynomial for >> > >> angles in Gromacs? I know I can use tables but wish to fit my data >> into >> > >> such a function. >> > >> >> > >> >> > > Nothing in the manual seems to suggest that such a form is supported. >> > > >> > > -Justin >> > > >> > >> > Would that be difficult to implement it into the code? >> > >> >> Not really, but since you can use a table to describe the functional form >> even for a bonded interaction (see manual) then you should do that. It's >> much better to prove the functional form is useful and works when you >> haven't touched the C code, and only touch the C code when it is clear that >> performance is an issue (which it probably isn't for any bonded >> interaction). >> >> Mark >> > > Thank you. I am trying to avoid tabulated potentials as much as I can so > hence my question.
Why? You're just making extra work. > Can you please write me where in Gromacs direcotry I > could possibly modify it to see the code? See src/gmxlib/bondfree.c. And then work out how to get your parameters read in from a .top file and written to an .tpr file and maintained in different data structures accordingly. Mark > > Steven > > >> >> > >> > > On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul <jalem...@vt.edu> >> wrote: >> > >> >> > >> >> > >>> >> > >>> On 6/5/13 8:40 AM, Steven Neumann wrote: >> > >>> >> > >>> Dear Gmx Users, >> > >>>> >> > >>>> I wish to use quartic angle potential and specify all constants. I >> > know >> > >>>> it >> > >>>> is a function 6 of [ angles ] but do not know how to place my >> > polynomial >> > >>>> constants? >> > >>>> >> > >>>> >> > >>>> As table 5.5 in the manual indicates, list the equilibrium angle >> > >>> followed >> > >>> by all of the constants, in order. >> > >>> >> > >>> -Justin >> > >>> >> > >>> -- >> > >>> ==============================****========== >> > >>> >> > >>> >> > >>> Justin A. Lemkul, Ph.D. >> > >>> Research Scientist >> > >>> Department of Biochemistry >> > >>> Virginia Tech >> > >>> Blacksburg, VA >> > >>> jalemkul[at]vt.edu | (540) 231-9080 >> > >>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin< >> > http://vt.edu/Pages/Personal/justin> >> > >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin< >> > 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< >> > http://lists.gromacs.org/**mailman/listinfo/gmx-users> >> > >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users< >> > http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>> > >> > >>> * Please search the archive at http://www.gromacs.org/** >> > >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >> > >>> Mailing_Lists/Search< >> > http://www.gromacs.org/Support/Mailing_Lists/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/****Support/Mailing_Lists< >> > http://www.gromacs.org/**Support/Mailing_Lists> >> > >>> <http://**www.gromacs.org/Support/**Mailing_Lists< >> > http://www.gromacs.org/Support/Mailing_Lists> >> > >>> > >> > >>> >> > >>> >> > > -- >> > > ==============================**========== >> > > >> > > Justin A. Lemkul, Ph.D. >> > > Research Scientist >> > > Department of Biochemistry >> > > Virginia Tech >> > > Blacksburg, VA >> > > jalemkul[at]vt.edu | (540) 231-9080 >> > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< >> > 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< >> > http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > > * Please search the archive at http://www.gromacs.org/** >> > > Support/Mailing_Lists/Search< >> > http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists< >> > http://www.gromacs.org/Support/Mailing_Lists> >> > > >> > -- >> > 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/Support/Mailing_Lists/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/Support/Mailing_Lists >> > >> -- >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >> > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
