AMBER Archive (2008)

Subject: Re: AMBER: Help with NMODE

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Fri May 02 2008 - 13:05:19 CDT

On Fri, May 2, 2008 at 1:06 PM, David A. Case <case_at_scripps.edu> wrote:

> 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.
> >
> >
>

It is only the 1-4 EEL that is different, and I am using a dielectric of 1.0
for both the sander and nmode. Thank you for the heads up, I will
investigate any further differences... hopefully I can find something.

>
> >
> > > > 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?
>
>
I am using Amber 8 with all of the latest bug fixes.

Thanks again,
Seth

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