Re: [AMBER] graph energy check after minimization

From: amor san juan <>
Date: Sat, 12 Jul 2014 11:03:44 +0100

hi Jason

Thanks so much for your reply and ideas. Above all your time and attention
given. I apologize for choosing the wrong word 'strange energy plots'. I
will closely study the manual and if anything is vague to me, i hope to
receive helpful feedback from the forum. Thanks for informing to try use
the ntmin command, and i will try on this.


On Fri, Jul 11, 2014 at 8:19 PM, Jason Swails <>

> On Jul 11, 2014, at 11:59 AM, amor san juan <> wrote:
> > HI all,
> >
> > Would someone please give a hint on what is the possible cause of my
> > strange energy plot during minimization. I attach the graphs in each 3
> > minimization tests. It seems that the protein did not successfully
> relaxed.
> > Could it be it due to amino acid clashes in the input file ? Or something
> > is not proper in my input scipt.
> Why do you say this is strange? Your input files all specify ncyc=500,
> which means the steepest descent algorithm is used to minimize for the
> first 500 steps (a very slowly converging algorithm). After that, the
> conjugate gradient method is used, which converges faster (which is why you
> see a sudden 'drop' about halfway through each plot).
> Other than that, all I can say is that most systems are composed of at
> least hundreds of atoms (if not several orders of magnitude more). With
> this many degrees of freedom, finding a local minimum is a real challenge,
> so there is no reason to suspect that 1000 steps of minimization with Amber
> will get you to a local minimum (or close enough to make it seem like the
> minimization is "done").
> That is rarely a problem, though, since minimization is typically used to
> relax bad contacts before starting dynamics -- proteins exist in room
> temperature, not at absolute zero, so exact local minima are not that
> important for most biomolecular simulations (there are some exceptions,
> like normal mode analyses).
> If you absolutely require a local minimum, you should look into the XMIN
> minimizer (ntmin=3, I think -- it should be described in the manual).
> Hope this helps,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat Jul 12 2014 - 03:30:03 PDT
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