Hello,
This is a very common error that has been widely discussed in the past (look
through the amber mailing archives). In fact, there was even a webpage
devoted to it: http://ambermd.org/Questions/linmin.html.
Basically, the standard amber minimizer is not good enough to do the type of
minimization you're asking it to do, since it got caught in a spot it
couldn't find its way out of. If you want to do a better minimization,
consider using XMIN (see the ntmin variable description in the amber
manual).
Good luck!
Jason
On Tue, Jan 11, 2011 at 8:11 AM, Jan Wahl <JanWahl.gmx.de> wrote:
> Dear community,
> i have a strange problem doing a conformation analysis using a python
> script and amber 11. I'm doing some minimizations using the following
> sander-input
>
>
> # Running minimization
> cat << eof > min.in
> # 200000 steps of minimization
> &cntrl
> maxcyc=200000, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
> /
>
>
>
>
>
> sander is started usuing the following commands
>
> sander -O -i sander.in -o out.out -p prmtop -c inpcrd
>
>
>
> in the following you can see the end of my outputfile
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 34000 -8.1184E+01 9.1854E-04 3.4484E-03 C4 54
>
> BOND = 2.1401 ANGLE = 20.5820 DIHED =
> 36.1946
> VDWAALS = -9.6894 EEL = -19.9560 EGB =
> -78.1446
> 1-4 VDW = 14.2583 1-4 EEL = -46.5690 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 35000 -8.1184E+01 1.2796E-03 5.0121E-03 N9 50
>
> BOND = 2.1400 ANGLE = 20.5812 DIHED =
> 36.1951
> VDWAALS = -9.6875 EEL = -19.9644 EGB =
> -78.1372
> 1-4 VDW = 14.2586 1-4 EEL = -46.5699 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 36000 -8.1184E+01 1.2446E-03 3.6949E-03 C6 56
>
> BOND = 2.1398 ANGLE = 20.5802 DIHED =
> 36.1955
> VDWAALS = -9.6849 EEL = -19.9872 EGB =
> -78.1156
> 1-4 VDW = 14.2590 1-4 EEL = -46.5709 RESTRAINT =
> 0.0000
>
> ... RESTARTED DUE TO LINMIN FAILURE ...
>
> ***** REPEATED LINMIN FAILURE *****
>
> ***** SEE http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
>
>
>
>
>
>
>
> the strnage behavior is now, that some minimizations will finish without
> this error and some will finish with this error.
>
>
> Can anyone give me some help in solving this problem???
> I appreciate your halp.
>
>
> Best reegards
>
>
> Jan Wahl
> Goethe University/ Germany
>
> --
> GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit
> gratis Handy-Flat! http://portal.gmx.net/de/go/dsl
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jan 11 2011 - 07:30:03 PST
