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 - 11:26:23 CDT

There are 12297 atoms. I have now looked at other successful minimizations
and the BOND energy values seem acceptable.
I am using serial sander from AMBER9.
I tested with
*cd $AMBERHOME/test/ && make test.serial
*There were a few cases under *qmm2* and *pbsa_radi* with different results
in the 4th decimal. At any rate, I am doing sander with explicit solvent.
All the other tests cleared.*
*

On Fri, Sep 5, 2008 at 11:23 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Jose,
>
>
>
> There doesn't look to be anything wrong here, although a bond energy of
> 4411 is pretty high, but then it is not clear how many atoms you have etc. I
> suspect the minimizer has gone as far as it can and should quit with a
> linmin error (your RMS is pretty low). However, it should not segfault.
>
>
>
> Is this in serial or parallel? Which version of AMBER are you using and
> have you applied all the bug fixes? Do all the test cases pass?
>
>
>
> All the best
>
> Ross
>
>
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Jose Borreguero
> *Sent:* Friday, September 05, 2008 8:07 AM
> *To:* amber mailing list
> *Subject:* AMBER: help...sander "segmentation fault" after 2hours of
> minimization
>
>
>
> Dear Amber users,
> 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?
> 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
> #Apply restraints to the solute atoms
> 1.0
> RES 55 63
> END
> END*
> Best regards,
> --
> Dr. 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
> 

-- 
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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