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.ambermd.org [mailto:amber-bounces.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.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.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.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Sep 18 2009 - 17:00:02 PDT
