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

Erik Lindahl lindahl at stanford.edu
Fri Aug 30 23:42:00 CEST 2002

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.



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