[gmx-users] (no subject)

David spoel at xray.bmc.uu.se
Mon Feb 21 22:02:21 CET 2005

On Mon, 2005-02-21 at 11:58 -0500, Dongsheng Zhang wrote:
> 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.
ffgmx2 is not a real force field. Please check opls in stead.

> 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
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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