Hi Dan,
thank you for your work. I also believe that my system is minimized.
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...
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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Received on Tue Jun 17 2014 - 14:30:03 PDT
