Why? To avoid refining and extrapolating 100 tables for a Coarse grained run and use constants instead... And to make it faster obviously.
On Wed, Jun 19, 2013 at 9:22 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > No. You're modifying the C code, so you will have to learn to maintain > a GROMACS installation. Yet another reason to avoid modifying the C > code :-) > > Mark > > On Wed, Jun 19, 2013 at 10:06 AM, Steven Neumann <s.neuman...@gmail.com> > wrote: > > I will speak to someone who is familiar with the code. However, my > Gromacs > > version is installed on the cluster, can I create a file in my directory > > which will use this code with a given potential? > > > > > > On Wed, Jun 19, 2013 at 8:41 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. 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 > -- > 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
