Re: NAN GRADIENT TOLERANCE - & - RESTARTING CONJUGATE GRADIENT ALGORITHM

From: Peter Spijker (pspijker_at_wag.caltech.edu)
Date: Thu May 20 2004 - 12:47:57 CDT

Brian (and others),

Thanks for helping me again. The point is that there are no output energies
or energies on several time steps. The simulation somehow simply won't
start. It is only complaining about the gradient tolerance and restarting
the algorithm. And yes, I am just minimizing the butoxamine on its own. So
what I did, I centered the butoxamine around 0,0,0 and made an .xsc file in
which I created a large enough box, so no bonds should be cut off. I doubt
it anyway that this might be the case, while the minimisation simply didn't
start, to my opinion. I can send you the pdb-, psf-, namd-, and inp-files if
you want them. I think I might have done something wrong with the
par_whatever.inp file, since I hade to add an entry, because there were no
angles and dihedrals present for the series: aromatic carbon - oxygen -
sp3carbon. I entered this as CA-OC-CT3. These are the two added lines to the
par_whatever.inp file (and within the angle and dihedral sections of
course):

CA OC CT3 65.000 108.00

CA CA OC CT3 3.1000 2 180.00

I have to do something wrong, but I cannot see why. Thanks for helping
again.

Peter Spijker
Caltech

----- Original Message -----
From: "Brian Bennion" <brian_at_youkai.llnl.gov>
To: "Peter Spijker" <pspijker_at_wag.caltech.edu>
Sent: Thursday, May 20, 2004 5:05 PM
Subject: Re: namd-l: NAN GRADIENT TOLERANCE - & - RESTARTING CONJUGATE
GRADIENT ALGORITHM

>
>
> Hi Peter,
> what do the final energies look like? Set your output energy to every
> step just to track it. I would suspect that the you are just minimizing
> the butoxamine? It is possible that your ligand isn't centered in its box
> and a bond or two is being cut off...
> The energy output will test this.
>
> Regards
> Brian
>
>
> On Thu, 20 May 2004, Peter Spijker wrote:
>
> > Hi all!
> >
> > At this very moment I am trying to adapt the top_whatever.inp and
> > par_whatever.inp files so I can run a protein structure with different
> > ligands, either antagonists or agonists. So far so good I managed to get
two
> > structures right (well, it worked, if it worked needs to be find out
yet).
> > These are for epinephrine and norepeniphrine. Now I am working on
butoxamine
> > (a antagonist), but I encounter some problems. This time no psfgen
> > problems, but something I do not understand from NAMD. The program does
not
> > complain about any missing parameters or something alike, but when
running a
> > minimisation it sends as output only this:
> >
> > INITIAL STEP: 1e-06
> > GRADIENT TOLERANCE: nan
> > BRACKET: 0 0 nan nan nan
> > RESTARTING CONJUGATE GRADIENT ALGORITHM
> > INITIAL STEP: 2.5e-07
> > GRADIENT TOLERANCE: nan
> > BRACKET: 0 0 nan nan nan
> > RESTARTING CONJUGATE GRADIENT ALGORITHM
> >
> > And so on, and so on.Only the initial steps become smaller and smaller.
> > Untill it fails and the program stops without writing any file
information.
> > Which seems okay, because the simulation actually never started. I do
not
> > get what might be wrong. The initial energies look not too bad:
> >
> > TCL: Minimizing for 2000 steps
> > ETITLE: TS BOND ANGLE DIHED
IMPRP
> > ELECT VDW BOUNDARY MISC KINETIC
> > TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
> >
> > ENERGY: 0 37.5420 544.9918 0.1572
0.0000
> > 54.5077 11.1455 0.0000 0.0000 0.0000
> > 648.3442 0.0000 648.3442 648.3442 0.0000
> >
> > Can anyone give me a clue what might be going on? It would be very
helpful I
> > think. Thank you all.
> >
> > Kind regards,
> >
> > Peter Spijker
> >
> > ---
> >
> > Peter Spijker
> >
> > Fulbright Fellow - The Netherland-America Foundation
> >
> > California Institute of Technology
> > Biochemistry & Molecular Biophysics
> > Materials Process and Simulation Center
> > MC 139-74 Caltech
> > Pasadena, CA-91125
> > The United States of America
> >
> > Phone: (626)-395-2844
> > E-mail: pspijker_at_wag.caltech.edu
> >
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>

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