AMBER Archive (2008)

Subject: Re: AMBER: Help with NMODE

From: David A. Case (
Date: Fri May 02 2008 - 12:06:33 CDT

On Fri, May 02, 2008, Seth Lilavivat wrote:
> Yes, I am getting a different energy in my first step of nmode than my last
> step of sander min. All of the terms are the same except for the
> Electrostatics term.

OK..that narrows it down at lot, although it is still puzzling. Do you mean
that just the EEL term is different, or is the 1-4 EEL term different as well?
If the vdw energy is identical in both codes, then you are looking at the same
pairlist; since the EEL and VDW energies are computed in the same loop, there
must be something like dielectric that is different. Are you sure you are not
using something like constant dielectric in one code and distance dependent in
the other? Be diligent in looking for differences related to electrostatics.
> > > I am also getting a "DIHEDRAL ANGLE ERROR." As an example I've pasted
> > the
> > > last part of my nmode.rec.1.out file:
> > >
> > >
> > > DIHEDRAL ANGLE ERROR: 10441788179118001803

Still confused here. I can't see from the code how you could possibly get
this error and still have identical dihedral angle energies as sander. Also,
the format of the error looks odd: which version of Amber are you using?


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