AMBER Archive (2009)

Subject: RE: [AMBER] LINMIN failure notice

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Sep 18 2009 - 18:41:33 CDT

FYI, This advice is completely wrong. The LINMIN failure has NOTHING to do
with availability of memory or stack size. See the correct answer by Prof.
Case in this same thread.

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Ashish Runthala
> Sent: Friday, September 18, 2009 3:46 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] LINMIN failure notice
>
> See the reason behind this erroris unallocation of memory space.
> Better increase the memory size of stack to run this.
> If you are windows user, increase virtual memory. Or if you are using
> linux, increase the stacksize.
>
> You may also remove trivial parameters from the run, to decrease the
> allocated memory requirement.
>
> On 9/18/09, Jio M <jiomm_at_yahoo.com> wrote:
> > Dear Amber users;
> >
> >
> >
> > I have ligand protein complex with waterbox.. I did minimisation with
> SHAKE
> > then this LINMIN failure came...
> >
> >
> >
> > but it was suggested to do first minimisation without SHAKE then
> second
> > minimisation with SHAKE..in this case I got no error in first
> > minimisation  but with SHAKE LINMIN failure again noticed.. what
> > is  reason and solution for this .......
> >
> >
> >
> > min_noSHAKE.in
> >
> >
> >
> >
> >
> >  &cntrl
> >
> >   imin=1,maxcyc=1000,ncyc=500,
> >
> >   cut=8.0,ntb=1,
> >
> >   ntc=1,ntf=1,
> >
> >   ntpr=100,
> >
> >   ntr=1, restraintmask=':207-478',
> >
> >   restraint_wt=2.0
> >
> >  /
> >
> >
> >
> > min.in file
> >
> >
> >
> > &cntrl
> >
> >   imin=1,maxcyc=1000,ncyc=500,
> >
> >   cut=8.0,ntb=1,
> >
> >   ntc=2,ntf=2,
> >
> >   ntpr=100,
> >
> >   ntr=1, restraintmask=':207-478',
> >
> >   restraint_wt=2.0
> >
> >  /
> >
> >
> >
> >  4.  RESULTS
> >
> > ---------------------------------------------------------------------
> -----------
> >
> >
> >
> >  ---------------------------------------------------
> >
> >  APPROXIMATING switch and d/dx switch using CUBIC SPLINE
> INTERPOLATION
> >
> >  using   5000.0 points per unit in tabled values
> >
> >  TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> >
> > | CHECK switch(x): max rel err =   0.2738E-14   at   2.422500
> >
> > | CHECK d/dx switch(x): max rel err =   0.8314E-11   at   2.736960
> >
> >  ---------------------------------------------------
> >
> > | Local SIZE OF NONBOND LIST =     507119
> >
> > | TOTAL SIZE OF NONBOND LIST =    7982221
> >
> >
> >
> >
> >
> >    NSTEP
> > ENERGY
> > RMS
> > GMAX
> > NAME    NUMBER
> >
> >       1
> > -1.5371E+05     1.8408E+01
> > 6.1403E+01
> > O        9015
> >
> >
> >
> >  BOND    =
> > 139.7029  ANGLE   =
> > 585.9775  DIHED
> > =     2697.3324
> >
> >  VDWAALS =    26288.8749
> > EEL     =  -196992.8151
> > HBOND
> > =        0.0000
> >
> >  1-4 VDW =      935.1457  1-4 EEL
> > =    12636.5467  RESTRAINT
> > =        1.3255
> >
> >  EAMBER  =  -153709.2350
> >
> >
> >
> >
> >
> >    NSTEP
> > ENERGY
> > RMS
> > GMAX
> > NAME    NUMBER
> >
> >     100
> > -1.5371E+05     1.8408E+01
> > 6.1382E+01
> > O        9015
> >
> >
> >
> >  BOND    =
> > 139.6206  ANGLE   =
> > 585.9935  DIHED
> > =     2697.3411
> >
> >  VDWAALS =    26285.6160
> > EEL     =  -196988.8291
> > HBOND
> > =        0.0000
> >
> >  1-4 VDW =      935.1360  1-4 EEL
> > =    12636.5486  RESTRAINT
> > =        1.3329
> >
> >  EAMBER  =  -153708.5731
> >
> >
> >
> >
> >
> >    NSTEP
> > ENERGY
> > RMS
> > GMAX
> > NAME    NUMBER
> >
> >     200
> > -1.5371E+05     1.8408E+01
> > 6.1382E+01
> > O        9015
> >
> >
> >
> >  BOND    =
> > 139.6198  ANGLE   =
> > 585.9938  DIHED
> > =     2697.3412
> >
> >  VDWAALS =    26285.5845
> > EEL     =  -196988.7917
> > HBOND
> > =        0.0000
> >
> >  1-4 VDW =      935.1359  1-4 EEL
> > =    12636.5488  RESTRAINT
> > =        1.3330
> >
> >  EAMBER  =  -153708.5677
> >
> >
> >
> >
> >
> >    NSTEP
> > ENERGY
> > RMS
> > GMAX
> > NAME    NUMBER
> >
> >     300
> > -1.5371E+05     1.8408E+01
> > 6.1382E+01
> > O        9015
> >
> >
> >
> >  BOND    =
> > 139.6190  ANGLE   =
> > 585.9939  DIHED
> > =     2697.3413
> >
> >  VDWAALS =    26285.5526
> > EEL     =  -196988.7510
> > HBOND
> > =        0.0000
> >
> >  1-4 VDW =      935.1358  1-4 EEL
> > =    12636.5484  RESTRAINT
> > =        1.3331
> >
> >  EAMBER  =  -153708.5599
> >
> >
> >
> >
> >
> >    NSTEP
> > ENERGY
> > RMS
> > GMAX
> > NAME    NUMBER
> >
> >     400
> > -1.5371E+05     1.8408E+01
> > 6.1382E+01
> > O        9015
> >
> >
> >
> >  BOND    =
> > 139.6181  ANGLE   =
> > 585.9941  DIHED
> > =     2697.3414
> >
> >  VDWAALS =    26285.5202
> > EEL     =  -196988.7128
> > HBOND
> > =        0.0000
> >
> >  1-4 VDW =      935.1358  1-4 EEL
> > =    12636.5483  RESTRAINT
> > =        1.3331
> >
> >  EAMBER  =  -153708.5548
> >
> >
> >
> >
> >
> >    NSTEP
> > ENERGY
> > RMS
> > GMAX
> > NAME    NUMBER
> >
> >     500
> > -1.5371E+05     1.8408E+01
> > 6.1382E+01
> > O        9015
> >
> >
> >
> >  BOND    =
> > 139.6174  ANGLE   =
> > 585.9943  DIHED
> > =     2697.3415
> >
> >  VDWAALS =    26285.4885
> > EEL     =  -196988.6745
> > HBOND
> > =        0.0000
> >
> >  1-4 VDW =      935.1357  1-4 EEL
> > =    12636.5485  RESTRAINT
> > =        1.3332
> >
> >  EAMBER  =  -153708.5486
> >
> >
> >
> >      .... RESTARTED DUE TO LINMIN FAILURE ...
> >
> >
> >
> >      .... RESTARTED DUE TO LINMIN FAILURE ...
> >
> >
> >
> >      .... RESTARTED DUE TO LINMIN FAILURE ...
> >
> >
> >
> >      .... RESTARTED DUE TO LINMIN FAILURE ...
> >
> >
> >
> >
> >
> >    NSTEP
> > ENERGY
> > RMS
> > GMAX
> > NAME    NUMBER
> >
> >     600
> > -1.5371E+05     1.8408E+01
> > 6.1382E+01
> > O        9015
> >
> >
> >
> >  BOND    =
> > 139.6171  ANGLE   =
> > 585.9943  DIHED
> > =     2697.3415
> >
> >  VDWAALS =    26285.4794
> > EEL     =  -196988.6632
> > HBOND
> > =        0.0000
> >
> >  1-4 VDW =      935.1357  1-4 EEL
> > =    12636.5486  RESTRAINT
> > =        1.3332
> >
> >  EAMBER  =  -153708.5465
> >
> >
> >
> >      .... RESTARTED DUE TO LINMIN FAILURE ...
> >
> >
> >
> >      ***** REPEATED LINMIN FAILURE *****
> >
> >
> >
> >      ***** SEE http://amber.scripps.edu/Questions/linmin.html FOR
> MORE INFO
> > *****
> >
> >
> >
> >
> >
> >                     FINAL RESULTS
> >
> >
> >
> >
> >
> >
> >
> >    NSTEP
> > ENERGY
> > RMS
> > GMAX
> > NAME    NUMBER
> >
> >     614
> > -1.5371E+05     1.8408E+01
> > 6.1382E+01
> > O        9015
> >
> >
> >
> >  BOND    =
> > 139.6171  ANGLE   =
> > 585.9943  DIHED
> > =     2697.3415
> >
> >  VDWAALS =    26285.4781
> > EEL     =  -196988.6617
> > HBOND
> > =        0.0000
> >
> >  1-4 VDW =      935.1357  1-4 EEL
> > =    12636.5486  RESTRAINT
> > =        1.3332
> >
> >  EAMBER  =  -153708.5463
> >
> >
> >
> > thanks:
> >
> > Jiomm
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Ashish Runthala,
> Faculty Division III,
> Assistant Lecturer, Biological Sciences,
> Birla Institute of Technology and Science,
> Pilani, Rajasthan- 333031
> INDIA
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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