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

[Steven Neumann]

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>
> > >>> >
> > >>>
> > >>> ==============================****==========
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> > >
> > > 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>
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