VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Jan 05 2018 - 12:23:30 CST

Sequence matters!!! From the CHARMM docs (io.doc)

There are five choices for wildcard usage for improper dihedrals;
1) A - B - C - D (all four atoms, double specification allowed)
2) A - X - X - B
3) X - A - B - C
4) X - A - B - X
5) X - X - A - B
When classifying an improper dihedral, the first acceptable match (from
the above order) is chosen. The match may be made in either direction
( A - B - C - D = D - C - B - A).

-Josh

On 01/05/2018 10:51 AM, Brian Radak wrote:
> 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 https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fonlinelibrary.wiley.com%2Fdoi%2F10.1002%2Fjcc.540040211%2Fepdf&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C56b37cdcd49b44df2c6a08d55464e3bd%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636507714661227831&sdata=0Ahnc7ofpIGDy5csf%2F0DPwg8nlAFPhNiby7Zm2Y7oQw%3D&reserved=0)