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

[Mark Abraham]

On Wed, Jun 19, 2013 at 9:41 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.

Why? You're just making extra work.

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

See src/gmxlib/bondfree.c. And then work out how to get your
parameters read in from a .top file and written to an .tpr file and
maintained in different data structures accordingly.

Mark

>
> 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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