Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems

From: Daniel Roe <>
Date: Sat, 14 Jun 2014 11:49:48 -0600


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?


On Thu, Jun 12, 2014 at 2:39 PM, David A Case <> 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.
> 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
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Sat Jun 14 2014 - 11:00:02 PDT
Custom Search