VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 15 2010 - 18:12:12 CST

On Sat, 2010-01-16 at 00:53 +0100, MyLinkka wrote:
> Hi Alex,

dear ting,

> To be honest, your explanation of improper angles is really new to me.

o dear. how long have you been using MD? have you never looked
at a paper describing the implementation a classical force field?

> But I still can't get your idea exactly. From the picture I showed you
> in previous post, it seems improper angle is really just a geometric

you should not infer from an image, but know from
its actual definition and use.

> definition,related to nothing else. If this is not true, could you
> please give an example what kinds of information other than bonding
> are NECESSARY in order to get impropers? (Let's always suppose the
> bonds are known.)

actually bonds are note really required for impropers. the whole
point of improper angle interactions is to ensure a geometry that
would otherwise not be possible to achieve with plain angles and
dihedrals. for example to keep systems of conjugated double bonds
planar. to decide whether this is the case, you need to know more
than just bonds and atoms, hence you cannot guess them.

cheers,
    axel.
>
> Ting
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.