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

[Mark Abraham]

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

>
> >  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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