Hi,
Is it because I do not use the latest version of AMBER but AMBER 12
instead? I get the following error when I try to run it with with
pmemd.cuda Version 12.3:
| New format PARM file being parsed.
| Version = 1.000 Date = 04/23/14 Time = 14:17:23
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
CUDA (GPU): Prmtop appears to contain modified off-diagonal elements for
VDW A coef.
GPU code does NOT support such force field modifications.
Found Aij = 787979.7920942737 expected
479622.7030000000
i = 20 j = 1 Matrix element = 191
Did anyone get negative dihedral energy with ff14ipq and AMBER 14?
thanks,
Thomas
On 28 April 2014 00:34, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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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>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Mon Apr 28 2014 - 02:30:03 PDT
