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. Can you please write me where in Gromacs direcotry I could possibly modify it to see the code? 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
