VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Oct 02 2013 - 08:04:29 CDT

Daniel,

The reason for the "noise" is most commonly due to coupled and/or contaminating interactions. In many cases, this can be alleviated by using a fragmentation approach to reduce the complexity of your molecule, particularly for molecules that have significantly 3D topologies. I'm not sure that there's an answer for what a "normal" noise level is, as this is dependent on the molecule. In our hands ffTK is extremely good at fitting dihedral PESs, even for coupled systems; however, I have observed cases where contaminating interactions (e.g. vdW) have eroded the quality of the fit.

I'm not familiar with the specifics for computing CMAP terms. If you don't hear from anyone on VMD-L, you might crosspost to the CHARMM forums, specifically the parameter set section.

Regards,
Christopher Mayne

On Oct 2, 2013, at 3:24 AM, Daniel Klose wrote:

> 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
>
>