[gmx-users] poly(lactic acid) .itp or .top file

[Erik Lindahl]

Chris O'Brien wrote:
> Hello all,
> 
> I am trying to develop an accurate topology file for poly(lactic acid). 
> Most features of the topology file are obvious, but I have some 
> questions about the dihedral parameters. How do I take quantum modeling 
> (MP2 and DFT level) information about the barrier for rotating the 
> dihedral angle and convert that into the parameters listed in the .itp 
> file?


This probably depends on your system; it's a little complicated since
the effective potential is influenced by the 1,4 interactions too.

There are essentially two options for fitting (in contrast to guessing):

1. Remove the 1,4 interactions completely and fit a Ryckaert-Bellemans
    form of dihedral (5 cosine terms) to your potential data.

2. Keep the 1,4 interactions, calculate the effect they have on
    the effective potential form, and fit a normal or Ryckaert-Bellemans
    dihedral to make the total effective potential as close to your
    QC data as possible.




> 
> Same question for the improper dihedrals.  How important is the force 
> constant value to successful modeling?  Can you just make it large to 
> discourage (for example) a change of chirality?  If it is important to 
> have these numbers accurately, does anybody know the best way to 
> calculate them?

Improper dihedrals are more or less intelligent guesses in most 
forcefields I know of :-) Check the values in the gromacs and gromos 
forcefields and pick something (OPLS does it slightly different since
the use a periodic cosine). If you make it way too low it won't have
any effect, and if you pick it way too high the molecule might slightly 
be too rigid.

Cheers,

Erik