• ## Outreach

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 13 2010 - 11:08:36 CST

On Wed, 2010-01-13 at 17:41 +0100, MyLinkka wrote:
> Hi Axel,
>
>
> I can understand to guess impropers just based on
> atom coordinates is ridiculous. But once the bonds,
> angles and dihedrals are already provided explicitly
> or guessed, I think the impropers should also be defined,

no, why?

> right? In this case no guess is needed.We can always
> define an improper with 4 atoms, i,j,k,l, with i the center
> and j,k,l connecting to i.In principle if the atoms
> positions and bonds are provided, we can write out all the
> internal coords. (bond/angle/dihedarl/improper). I don't

with this logic in mind, please explain what would be the
difference between an improper and a dihedral.

> really understand why you say improper must be give
> explicitly? Could you please explain it further?

have a look at what impropers are used for!

you need to know more about the system and
the force field to place impropers. there is
no way to guess them from topology alone. to
a lesser degree this is true for bonds, angles,
and dihedrals. this is why i called those subcommands
_guess_something to indicate some vagueness and
need to recheck.

cheers,
axel.

> Ting
>
>
> Axel Kohlmeyer wrote:
> > On Wed, 2010-01-13 at 15:28 +0100, MyLinkka wrote:
> >
> >> Hello, Axel,
> >>
> >
> > hello ting,
> >
> >
> >> Will there be a guessimpropers function in this plugin?
> >>
> >
> > no. never.
> >
> >
> >> I didn't find it in v1.1 and neither in the todo list in README
> >>
> >
> > please think about it for a little bit, and then
> > you should realize that impropers always have to
> > be given explicitly, or would at least need very
> > special heuristics for specific cases.
> >
> >
> >> Thanks for making this useful tool!
> >>
> >
> > you're most welcome. it has been fun writing it.
> > i only wish i had more time for working on it. :-(
> > there is still so much that could be done.
> >
> > cheers,
> > axel.
> >
> >
> >> Ting
> >>
> >
> >

```--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology