VMD-L Mailing List

From: Daniel Klose (daniel.klose_at_uni-osnabrueck.de)
Date: Wed Oct 02 2013 - 03:24:38 CDT

Dear VMD & ffTK Users,

two short questions that puzzle me:

First one regarding ffTK dihedral fitting:
I used ffTK on several small organic molecules so far and it worked really well!! Only now in one example for some reason I could not find so far, during the dihedral fitting procedure the initial MM energy (MMEi) seems awfully noisy and not a smooth as usually.

See red line in this plot: www.israfil.de/files/ffTK_dihedral_opt_problem.png

So in the end, the final energy profile will also be noisy because the dihedral terms only add smooth funtions.
What noise/variation level would be normal? What may be the reason for this "noise"?
I tried repeating the fitting of the bonded interactions, but always got the same results with different initial parameters.

All qm calculation were run with the default level of theory from ffTK and converged fine (normal termination and non-imaginary frequencies in the hessian calculation).

The second question is probably simpler:
I'd like to also compute cmap term, i.e. the correction matrices that give the dihedral-dependent offset energy to be added to the MM energy to better match the QM energy landscape.
My question is: Should I compare energies for exactly the same stuctures (and equal dihedrals) or should I compare energies between relaxed QM and relaxed MM structures with the dihedrals fixed to the cmap grid values?
And how should the scaling of the energies be done to calculate the matrices once the target qm data is obtained?

Thank you for your help & advice!! :)
Daniel