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-- > > > ---------------------------------------------------------------------------- ---- > 5. TIMINGS > ---------------------------------------------------------------------------- ---- > > |>>>>>>>>PROFILE of Average TIMES>>>>>>>>> > | Calc gb radii 16189.86 (16.22% of Gen B) > | Communicate gb radii 9742.64 ( 9.76% of Gen B) > | Calc gb diag 30491.24 (30.55% of Gen B) > | Calc gb off-diag 43341.16 (43.43% of Gen B) > | Other 36.38 ( 0.04% of Gen B) > | Gen Born time 99801.28 (100.0% of Nonbo) > | Nonbond force 99805.12 (93.87% of Force) > | Bond/Angle/Dihedral 567.36 ( 0.53% of Force) > | FRC Collect time 3246.43 ( 3.05% of Force) > | Other 2705.11 ( 2.54% of Force) > | Force time 106324.02 (96.79% of Runmd) > | Shake time 142.10 ( 0.13% of Runmd) > | Verlet update time 1312.72 ( 1.20% of Runmd) > | CRD distribute time 2024.34 ( 1.84% of Runmd) > | Other 46.02 ( 0.04% of Runmd) > | Runmd Time 109849.19 (100.0% of Total) > | Total time 109849.61 (100.0% of ALL ) > > | Number of list builds : 0 > > | Highest rstack allocated: 0 > | Highest istack allocated: 0 > | Job began at 12:25:01.582 on 09/30/2010 > | Setup done at 12:25:01.995 on 09/30/2010 > | Run done at 18:55:51.337 on 10/01/2010 > | wallclock() was called70000034 times > > ********************************************************** > ********************************************************** > ************************************* > > but some jobs are not getting terminated and sander is still running. last > few lines of output files are > > ********************************************************** > ********************************************************** > ************************************* > KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000 > > NSTEP = 2000000 TIME(PS) = 7000.000 TEMP(K) = 315.15 PRESS = > 0.0 > Etot = -1560.7726 EKtot = 1575.9914 EPtot = > -3136.7640 > BOND = 453.3646 ANGLE = 1121.0840 DIHED = 1353.4213 > 1-4 NB = 429.5338 1-4 EEL = 6447.2781 VDWAALS = -660.5796 > EELEC = -9440.4416 EGB = -2840.4245 RESTRAINT = > 0.0000 > ---------------------------------------------------------------------------- -- > > > A V E R A G E S O V E R 2000000 S T E P S > > > NSTEP = 2000000 TIME(PS) = 7000.000 TEMP(K) = 313.91 PRESS = > 0.0 > Etot = -1365.2274 EKtot = 1569.7995 EPtot = > -2935.0268 > BOND = 401.0967 ANGLE = 1146.3664 DIHED = 1336.4671 > 1-4 NB = 442.5130 1-4 EEL = 6372.6617 VDWAALS = -667.6084 > EELEC = -8967.0383 EGB = -2999.4850 RESTRAINT = > 0.0000 > ---------------------------------------------------------------------------- -- > > > R M S F L U C T U A T I O N S > > > NSTEP = 2000000 TIME(PS) = 7000.000 TEMP(K) = 5.35 PRESS = > 0.0 > Etot = 119.4705 EKtot = 26.7405 EPtot = > 117.8487 > BOND = 16.8868 ANGLE = 25.1935 DIHED = > 18.0292 > 1-4 NB = 10.0793 1-4 EEL = 55.0170 VDWAALS = > 28.5748 > EELEC = 329.2162 EGB = 208.3778 RESTRAINT = > 0.0000 > ---------------------------------------------------------------------------- -- > > ********************************************************** > ********************************************************** > ************************************** > > the output file is stuck there and sander is showing running...i am not able > to understand the problem should i terminate the job as 7 ns of simulation > is complete? thank you for the reply. > > -- > Nicholus Bhattacharjee > PhD Scholar > Department of Chemistry > University of Delhi > Delhi-110007 (INDIA) > Phone: 9873098743(M) > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Oct 01 2010 - 12:00:04 PDT