On Tue, Jun 17, 2014 at 3:15 PM, Guqin Shi <shi.293.osu.edu> wrote:
> Although it's only minimized to 10^-3. But forgive me, what does that mean
> by "running it with MD and found that not to be the case"? All the frames
> were retrieved from MD trajectories. For those structures which have been
> successfully minimized to under 10^-3, I did nmode calculation and from the
> output files, they seem pretty good...in terms of entropy. If you mean if
> I did other proteins with NAB, this is my first case...
>
Sorry, I should have been clearer. I was asking if you had subsequently
used the minimized structures (which it seems you have) and found any
issues related to poor minimization (which it seems you haven't). So it
seems like everything is OK.
-Dan
>
> Best,
> Guqin
>
>
> 2014-06-14 13:49 GMT-04:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
> > Hi,
> >
> > Based on the NAB output you provided, it looks like the energy reaches
> > a stable value around iteration 3917, after which point both the
> > energy and the gradient stop changing. I suspect what may be happening
> > is that the algorithm can't minimize the energy further so it doesn't
> > update the gradient array, leading to the previous gradient values
> > begin used to compute the total gradient again (which is why you get
> > the same RMSG value over and over). As a result the overall gradient
> > never gets smaller and so never triggers the tolerance criterion.
> >
> > I'll continue looking into the code (the XMIN code is fairly complex
> > so it may take a while) but I think you can be pretty confident that
> > your system is well-minimized. Have you tried running it with MD (or
> > performed a normal mode calc or something) and found that not to be
> > the case?
> >
> > -Dan
> >
> > On Thu, Jun 12, 2014 at 2:39 PM, David A Case <case.biomaps.rutgers.edu>
> > wrote:
> > > On Thu, May 29, 2014, Guqin Shi wrote:
> > >>
> > >> I didn't receive any reply from moderator. I upload .nab, .job,
> .prmtop,
> > >> .pdb, and .out file for one of my stuck frame in my dropbox public
> > folder.
> > >> You can see in .out file, starting from 3000+ step, it keeps at a
> single
> > >> rmsg and the energy remains unchanged.
> > >>
> > >> https://www.dropbox.com/sh/sa06jqcrciyjppp/AACBNlWwmaFuYWCvNdVunHrya
> > >
> > > I haven't forgotten about this, but I haven't solved the problem
> either.
> > > You may have to look closely at what might be different between frames
> > that
> > > work and those that get stuck (happens to me, too, even with Newton
> > Raphson
> > > minimization.) You might try turning off GB to see that changes the
> > behavior.
> > > But I don't have any obvious ideas. Maybe Dan Roe (or others)
> > > will see something I've missed.
> > >
> > > ...regards...dac
> > >
> > >
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> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
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> >
> >
> >
>
>
> --
> Guqin SHI
> The Ohio State University
> College of Pharmacy
> 500 W. 12th Ave.
> Columbus, OH, 43210
> (614)688-3531
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jun 19 2014 - 14:30:03 PDT
