sir,
I am beginner in amber. I am trying to run mm-pbsa. In the tutorial of
mm-pbsa in the below link
http://ambermd.org/tutorials/advanced/tutorial3/section1.htm
i found problem in the min.out file. it showes " ... RESTARTED DUE TO
LINMIN FAILURE ..." after 500 step.the file is as below.the
http://ambermd.org/tutorials/advanced/tutorial3/files/equil.tar.gz
out put file supplied in the website tutorial ,min.out is also have same
problem..."... RESTARTED DUE TO LINMIN FAILURE ...". please tell me the
solution to generate a right output file.
i am using amber V-2011
the output files supplied in website are generated from amber V-2009.
Is it a problem for to generate a same output file?
min.out:-
> RESTRAINT = 34.6928
EAMBER = -122741.3567
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -1.2271E+05 1.3808E+01 4.4786E+01 O 35909
BOND = 161.2707 ANGLE = 665.8085 DIHED =
2342.3925
VDWAALS = 6114.0079 EEL = -141295.3964 HBOND =
0.0000
1-4 VDW = 770.0934 1-4 EEL = 8500.4771 RESTRAINT =
34.6929
EAMBER = -122741.3464
NSTEP ENERGY RMS GMAX NAME NUMBER
300 -1.2271E+05 1.3808E+01 4.4786E+01 O 35909
BOND = 161.2706 ANGLE = 665.8080 DIHED =
2342.3923
VDWAALS = 6113.9971 EEL = -141295.3718 HBOND =
0.0000
1-4 VDW = 770.0933 1-4 EEL = 8500.4769 RESTRAINT =
34.6930
EAMBER = -122741.3336
NSTEP ENERGY RMS GMAX NAME NUMBER
400 -1.2271E+05 1.3808E+01 4.4786E+01 O 35909
BOND = 161.2704 ANGLE = 665.8074 DIHED =
2342.3921
VDWAALS = 6113.9838 EEL = -141295.3462 HBOND =
0.0000
1-4 VDW = 770.0932 1-4 EEL = 8500.4766 RESTRAINT =
34.6931
EAMBER = -122741.3227
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -1.2271E+05 1.3808E+01 4.4786E+01 O 35909
BOND = 161.2703 ANGLE = 665.8069 DIHED =
2342.3919
VDWAALS = 6113.9730 EEL = -141295.3223 HBOND =
0.0000
1-4 VDW = 770.0932 1-4 EEL = 8500.4767 RESTRAINT =
34.6932
EAMBER = -122741.3104
... 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 -1.2271E+05 1.3808E+01 4.4786E+01 O 35909
BOND = 161.2702 ANGLE = 665.8068 DIHED =
2342.3918
VDWAALS = 6113.9699 EEL = -141295.3146 HBOND =
0.0000
1-4 VDW = 770.0931 1-4 EEL = 8500.4765 RESTRAINT =
34.6932
EAMBER = -122741.3062
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
614 -1.2271E+05 1.3808E+01 4.4786E+01 O 35909
BOND = 161.2702 ANGLE = 665.8068 DIHED =
2342.3918
VDWAALS = 6113.9696 EEL = -141295.3137 HBOND =
0.0000
1-4 VDW = 770.0931 1-4 EEL = 8500.4765 RESTRAINT =
34.6933
EAMBER = -122741.3057
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.05 ( 0.02% of Total)
| Build the list 0.30 (59.16% of List )
| Other 0.21 (40.84% of List )
| List time 0.51 ( 0.23% of Nonbo)
| Short_ene time 166.44 (98.45% of Direc)
| Other 2.61 ( 1.55% of Direc)
| Direct Ewald time 169.05 (76.86% of Ewald)
| Adjust Ewald time 2.01 ( 0.91% of Ewald)
| Fill Bspline coeffs 2.23 ( 4.59% of Recip)
| Fill charge grid 5.42 (11.19% of Recip)
| Scalar sum 11.11 (22.94% of Recip)
| Grad sum 9.63 (19.88% of Recip)
| FFT time 20.05 (41.39% of Recip)
| Other 0.00 ( 0.01% of Recip)
| Recip Ewald time 48.44 (22.02% of Ewald)
| Virial junk 0.12 ( 0.06% of Ewald)
| Other 0.31 ( 0.14% of Ewald)
| Ewald time 219.94 (99.77% of Nonbo)
| Nonbond force 220.45 (98.61% of Force)
| Bond/Angle/Dihedral 3.05 ( 1.36% of Force)
| Other 0.07 ( 0.03% of Force)
| Force time 223.56 (100.0% of Runmd)
| Runmd Time 223.56 (98.87% of Total)
| Other 2.50 ( 1.11% of Total)
| Total time 226.12 (100.0% of ALL )
| Highest rstack allocated: 2363581
| Highest istack allocated: 42193
| Final Performance Info:
| -----------------------------------------------------
| Average timings for all steps:
| Elapsed(s) = 225.52 Per Step(ms) = 225521.12
| ns/day = 0.00 seconds/ns = **********
| -----------------------------------------------------
| Job began at 18:05:26.994 on 08/08/2017
| Setup done at 18:05:27.589 on 08/08/2017
| Run done at 18:09:13.110 on 08/08/2017
>| wallclock() was called 23383 times
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Received on Wed Aug 09 2017 - 08:30:03 PDT
