[gmx-users] (no subject)

[Dongsheng Zhang]

Dear Gromacs users,

I'm trying to understand the force fields, and their implementation in 
Gromacs.
Everything seems clear except for the improper dihedrals, which I'm
struggling to understand.
As an example, I'm looking to the ffgmx2* files. In particular, I'm
concentrating in the [ALA] description.

In the [ impropers ] section of [ALA], there are three impropers:
N  -C  CA   H
-C  -CA  N  -O
CA   N   C  CB

After playing with my plastic chemistry model, I'm almost convinced
that I understood why those are improper torsional angles, but there is
another one that looks improper too:

              CA   N   C  HA

What happen with this one? 

Also, the third improper (CA N C CB) could also be CA N CB C or CA CB C
N. I will guess a reason: The inner two atomes (N, C) form the common
edge for two triangles, and they are on the backbone. CA goes first
because it is the central atom in the triangle N CA C. Is that correct?
Could you please tell me how to make the sequence of four atoms in the
dihedral? 


I went through the manual, but didn't find an answer to this questions.
If there is a book/paper/web page explaining this, please let me know.

Thank you very much



-- 
Dongsheng Zhang <dong at pampas.chem.purdue.edu>