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

[Mark Abraham]

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>
>>> > >>> >
>>> > >>>
>>> > >>> ==============================****==========
>>> > >>>
>>> > >>> --
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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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