VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Jan 05 2018 - 10:40:00 CST

The order may not matter, but I'm pretty sure the sequence does. I don't
have the test case in front of me, but I recall changing the improper
definition and getting different energies for the same structure. This was
especially annoying with CGenFF because many of the old carboxylate force
fields use different atoms in the protonated and deprotonated states.
Defining correct alchemical topologies became a bit of a chore.

HTH,
Brian

On Wed, Jan 3, 2018 at 4:15 AM, Jadzia Dax <jadziadax30_at_gmail.com> wrote:

> Dear Peter,
>
> Thank you very much for your detailed answer, it has been extremely
> insightful.
>
> Since I guess one cannot change the behavior of psfgen in this regard the
> most simple solution might to be write a script which corrects the atom
> ordering in the psf-files to the default CHARMM format (central atom first)
> so that programs like CP2K are able to use it along with the original
> parameter files.
>
> Best wishes,
> Jadzia
>
>
>
>
> On Tue, Jan 2, 2018 at 4:31 PM, Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> Dear Jadzia,
>> The reason that the order is reversible is that the way the improper
>> potential is defined is based on the angle between the plane containing the
>> first three atoms, and the plane containing the second three atoms (see
>> Fig. 2 of http://onlinelibrary.wiley.com/doi/10.1002/jcc.540040211/epdf)--001a1144725088dd2f05620a19f1--