AMBER Archive (2008)

Subject: Re: AMBER: help...sander "segmentation fault" after 2hours of minimization

From: Jose Borreguero (borreguero_at_gmail.com)
Date: Fri Sep 05 2008 - 10:43:39 CDT

Total energy decreased from -45404.6511 to -57070.4772.
Minimal RMS=0.000721 at time_step=20100 (still higher than limit_RMS=0.0005)
Is there an automatic way to flag a high-energy bond ? This is a solvated
system with 14000 atoms :)

On Fri, Sep 5, 2008 at 11:20 AM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Fri, Sep 05, 2008, Jose Borreguero wrote:
>
> > I am trying to understand what went wrong with my minimization. The last
> > lines of the output file do not indicate anything weird going on, or
> maybe
> > the BOND energy term is indicating somethin (at the beginning of the
> > minimization, BOND=115.7477 and at the end, BOND*=4411.3524 *).
> > Where else should I look for pointers to the problem?
>
> It is the *total* energy that is minimized -- did that go downhill from
> the starting point?
>
> It looks like your minimization may have converged, reaching an rms of
> less than 0.0005, at some step after the last printed step. If so,
> there is no reason, per se, to think that something is wrong. You can
> examine the structure to see if there are individual bonds that are
> leading to the large-ish bond energy, and so on.
>
> ...dac
>
> > Here are the last lines of the output file:
> > *NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 20150 -5.7069E+04 1.1228E-03 4.5015E-02 H1 9884
> >
> > BOND = 4411.3524 ANGLE = 93.5743 DIHED =
> > 212.3167
> > VDWAALS = 10160.1516 EEL = -75579.7172 HBOND =
> > 0.0000
> > 1-4 VDW = 156.0090 1-4 EEL = 3475.8361 RESTRAINT =
> > 1.9324
> > EAMBER = -57070.4772*
> > And here's the input file:
> > *&cntrl
> > imin=1, maxcyc=100000, ntmin=0, ntr=1,
> > cut=10.0, nsnb=10, ntc=1, ntf=1, drms=0.0005
> > &end
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-- 
Jose M. Borreguero
Postdoctoral Associate
Oak Ridge National Laboratory
P.O. Box 2008, M.S. 6164
Oak Ridge, TN 37831
phone: 865-241-3071 fax: 865-576-5491
Email: borreguerojm_at_ornl.gov

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