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

Mark Abraham mark.j.abraham at gmail.com
Wed Jun 19 14:47:19 CEST 2013 

On Wed, Jun 19, 2013 at 10:30 AM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Why? To avoid refining and extrapolating 100 tables for a Coarse grained
> run and use constants instead...


I'd still think writing the script in your language of choice to write out
the tables is a much lighter weight proposition than setting up the
machinery to build and read the equivalent [angletypes] database. And a
table is much easier to drop in a graph in a publication to show the
reviewer you did it right.

And to make it faster obviously.
>

That doesn't matter until you know the functional form is a good one to
use. So we'll assume that for here and now. Then you'd want to know that an
existing equivalent coarse-grained simulation spends at least 10% of its
time on its bonded interactions. Because unless that's true, even if half
the interactions are angles that now take twice the time because they're
tabulated, one is still not optimizing anything important.

Mark

>
> 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>
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> > >>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > >>> > >>> >
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