Re: [AMBER] Deleting Box info from trajectory

From: Kshatresh Dutta Dubey <>
Date: Sun, 15 Jun 2014 10:47:00 +0300

Thanks for nice and detailed explanation.


On Sun, Jun 15, 2014 at 8:03 AM, Jason Swails <>

> On Sat, Jun 14, 2014 at 11:53 PM, Kshatresh Dutta Dubey <
> > wrote:
> > Okay Sir, I will do it, but following Gaussian output may, perhaps, make
> > clear what I want to say, this is output of Gaussian for normal
> termination
> > of every sander minimization step:
> > *Maximum Force 0.129720 0.000450 NO*
> > * RMS Force 0.019740 0.000300 NO*
> > * Maximum Displacement 0.095943 0.001800 NO*
> > * RMS Displacement 0.021493 0.001200 NO*
> > * Predicted change in Energy=-5.123724D-02*
> >
> > and Gaussian adds this energy to sander output. So how one can believe
> > that it is optimizing the system when proper convergence is not achieved.
> >
> ​Do these values never change? Or is the "NO" part what you find
> concerning? I'll repeat what others have said here -- Gaussian does NOT
> have any control over coordinates when used by sander -- it is ONLY used to
> compute energies and forces (the gradient of the potential) on the QM
> region in the presence of point charges representing the atoms of the MM
> region. In fact, Gaussian does not even compute all of the energies and
> forces for the atoms in the QM region -- MM atoms interact with QM atoms
> via the standard Lennard-Jones potential, so Gaussian does not even know
> about all forces acting on the QM atoms. Therefore, Gaussian should _not_
> be doing any minimizations (since only sander has all of the information).
> Most importantly, what this means is that Gaussian, in general, *will not*
> ever think an optimized geometry is reached, *even when it is* (unless the
> entire system is QM -- in which case just use Gaussian). This is because
> Gaussian does not know about all of the interactions taking place. Like
> others have said, sander just asks Gaussian to do what is necessary to
> obtain the information sander needs to perform its tasks (which is
> basically a set of energies and forces for atoms in the QM region in a
> field of MM charges). sander is the master that is contracting out work to
> Gaussian (and geometry optimization is _not_ in Gaussian's job description
> here).
> I will say that in general, the minimizers in sander are worse than the
> minimizers in ab initio programs like Gaussian. So it will take longer to
> achieve "convergence" with sander than it will if you are strictly using
> the Gaussian optimizers. If an optimized geometry is important, look into
> better minimizers (like the XMIN minimizers, described in the manual). If
> all you want to do is prepare to run dynamics, reaching a true minimum is
> not important.
> ​​
> > Is it Ok, and can I trust that Gaussian is doing well here?
> >
> You shouldn't blindly trust results you get from any program. They should
> make sense to you. If they don't make sense, it's either because: a) some
> assumption you made when predicting what could happen is wrong. b) You made
> a mistake in your input. or c) there is a bug in the program. It is safer
> to assume either (a) or (b), although (c) can happen on occasion, too. But
> it's time to trust that Gaussian does not -- and should not -- ever do
> geometry optimizations when used in the sander QM external interface. And
> even better, understand why that is true.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

With best regards
Dr. Kshatresh Dutta Dubey
Post Doctoral Researcher,
c/o Prof Sason Shaik,
Hebrew University of Jerusalem, Israel
Jerusalem, Israel
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Received on Sun Jun 15 2014 - 01:00:02 PDT
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