Dear community,
I am running some 7 ns simulation of protein in a
remote cluster. Some jobs have come out with as usual output file (bellow
shown last few lines of output):
************************************************************************************************************************************************************
R M S F L U C T U A T I O N S
NSTEP = 2000000 TIME(PS) = 7000.000 TEMP(K) = 5.48 PRESS =
0.0
Etot = 110.4493 EKtot = 27.4115 EPtot =
108.9311
BOND = 17.1038 ANGLE = 25.4147 DIHED =
18.7004
1-4 NB = 10.4789 1-4 EEL = 68.9331 VDWAALS =
22.4115
EELEC = 376.2388 EGB = 257.4596 RESTRAINT =
0.0000
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
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)
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Received on Fri Oct 01 2010 - 10:00:03 PDT
