VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Fri Nov 30 2012 - 09:15:08 CST

Yep.

The dihedral optimizer will allow you to optimize one or more dihedrals. Just remove the dihedrals that you already have parameters for form the "Dihedral Parameter Settings" box.

One thing to be careful with is that a given torsion is comprised of >1 dihedrals (well, most of the time anyway. hydrogen peroxide is an exception). When there is a limited torsional QM target data, it is difficult to fully deconvolute the individual contributions of each dihedral to a given torsion. This means that the optimized dihedrals accurately represent the torsions that you've directly parameterized, but there's no guarantee that the parameters are transferable. Just keep this in mind when parameterizing dihedrals that are involved in linkers.

Chris

On Nov 30, 2012, at 12:23 AM, ehsan zahedinejad wrote:

> Dear VMD users,
>
> I used VMD force field tool kit to develop ff for one monomer. To make a long chain of polymer I planned to find dihedral of connected bonds between monomers using Opt. torsion option of fftk without re-optimizing those dihedral that I already developed for monomers. Is there any way to use fftk to handle this problem. Should I just take out all those dihedrals parameters that I don't want to optimize from optimization procedure.
>
> I appreciate your responses.
> Cheers,
> Ehsan.