[gmx-users] Quartic angle potential - how to use?

[Steven Neumann]

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.abraham at 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.neumann08 at 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.neumann08 at gmail.com
> >wrote:
> >
> >>
> >>
> >>
> >> On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
> >>
> >>> On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann <s.neumann08 at gmail.com
> >>> >wrote:
> >>>
> >>> > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul <jalemkul at 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 <jalemkul at 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 at 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-request at 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 at 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-request at 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 at 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-request at gromacs.org.
> >>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>> >
> >>> --
> >>> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>
> >>
> > --
> > gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>