On Apr 27, 2014, at 3:42 PM, Thomas Evangelidis <tevang3.gmail.com> wrote:
> Dear AMBER list,
>
> I set up a simulation of a protein in TIP4P-Ew water using the new
> AMBER14ipq ff. I ran a few nanosecods to compute the accelerated MD
> parameters and noticed that the dihedral energy is always negative. I get
> the same results using both AMBER 12 pmemd CPU version and NAMD 2.10. This
> is the first time I encounter this with an AMBER ff and I wonder if it is
> normal. If yes, then I guess the empirical rules for selecting the dihedral
> boost in aMD are invalid.
This is strange in my experience as well, although to be fair I’ve never used the iPolQ force field myself.
It’s certainly not _illegal_ for torsion energies to be negative since the basis set of terms for the Fourier expansions are sines and cosines which take any value between -1 and 1. (Bond, angle, and CHARMM improper torsions, on the other hand, are quadratic and have a minimum energy of 0 at the equilbrium geometry).
I’m not terribly familiar with the details of running aMD (general knowledge of the theory is not enough to tell you how to run an effective simulation here), but the _true_ torsion potentials are actually the sum of the dihedral energy plus the 1-4 vdW and 1-4 electrostatic energies as well. Perhaps you can try some other combination of these terms in the empirical rules you were using?
Anyway, good luck!
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Apr 27 2014 - 15:00:02 PDT
