From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Wed Mar 09 2016 - 15:22:25 CST
Dear all,
I want to minimize and equilibrate a hyperbranched polymer in water. But,
calculations will be stopped after a few minutes and there is following
error in .log file.
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 2000
WRITING COORDINATES TO DCD FILE G2_wb_ion_eq.dcd AT STEP 2000
WRITING COORDINATES TO RESTART FILE AT STEP 2000
FINISHED WRITING RESTART COORDINATES
The last position output (seq=2000) takes 0.008 seconds, 265.543 MB of
memory in use
WRITING VELOCITIES TO RESTART FILE AT STEP 2000
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=2000) takes 0.003 seconds, 265.688 MB of
memory in use
REINITIALIZING VELOCITIES AT STEP 2000 TO 298 KELVIN.
TCL: Running for 1000000 steps
PRESSURE: 2000 -nan -nan -nan -nan -nan -nan -nan -nan -nan
GPRESSURE: 2000 -nan -nan -nan -nan -nan -nan -nan -nan -nan
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 2000 325637.0232 42912.9306 1189.1586
15.4447 -520807.4039 45269682.3750 0.0000
0.0000 -nan -nan -nan
45118629.5282 nan -nan -nan
-nan 74880.0000 -nan -nan
ERROR: Atom 199 velocity is 17801.6 11127 -16262.3 (limit is 12000, atom
2702 of 2844 on patch 2 pe 8)
ERROR: Atom 491 velocity is -141448 -73225.6 126785 (limit is 12000, atom
2761 of 2844 on patch 2 pe 8)
ERROR: Atom 492 velocity is -126367 -80506.7 115355 (limit is 12000, atom
2762 of 2844 on patch 2 pe 8)
ERROR: Atom 488 velocity is 20028.6 920.014 -13818.9 (limit is 12000, atom
2767 of 2844 on patch 2 pe 8)
ERROR: Atoms moving too fast; simulation has become unstable (4 atoms on
patch 2 pe 8).
ERROR: Exiting prematurely; see error messages above.
====================================================
WallClock: 433.247589 CPUTime: 433.247559 Memory: 261.957031 MB
ERROR: Atom 180 velocity is -1734.23 -12347.4 11551.3 (limit is 12000, atom
39 of 2858 on patch 4 pe 4)
ERROR: Atom 181 velocity is -2087 -13689.1 12186 (limit is 12000, atom 40
of 2858 on patch 4 pe 4)
ERROR: Atom 182 velocity is -3381.8 -5674.71 -18399.6 (limit is 12000, atom
41 of 2858 on patch 4 pe 4)
ERROR: Atom 194 velocity is 2618.66 16571.5 -15393.7 (limit is 12000, atom
53 of 2858 on patch 4 pe 4)
ERROR: Atom 195 velocity is 935.877 9289.25 -8706.76 (limit is 12000, atom
54 of 2858 on patch 4 pe 4)
ERROR: Atom 451 velocity is -105117 103665 -44039.6 (limit is 12000, atom
137 of 2858 on patch 4 pe 4)
ERROR: Atom 452 velocity is 48934.7 90886.3 273392 (limit is 12000, atom
138 of 2858 on patch 4 pe 4)
ERROR: Atom 476 velocity is 10656.7 1376.88 -7080.04 (limit is 12000, atom
2761 of 2858 on patch 4 pe 4)
ERROR: Atoms moving too fast; simulation has become unstable (8 atoms on
patch 4 pe 4).
ERROR: Atom 508 velocity is -13689.2 -6805.49 10929.8 (limit is 12000, atom
17 of 2823 on patch 1 pe 7)
ERROR: Atom 509 velocity is -15133.7 -8687.5 12138.9 (limit is 12000, atom
18 of 2823 on patch 1 pe 7)
ERROR: Atom 517 velocity is 65521 -33562.5 -111317 (limit is 12000, atom 23
of 2823 on patch 1 pe 7)
ERROR: Atom 523 velocity is 15123 7925.82 -15067.3 (limit is 12000, atom 29
of 2823 on patch 1 pe 7)
ERROR: Atom 524 velocity is 11632.3 8009.09 -10023.2 (limit is 12000, atom
30 of 2823 on patch 1 pe 7)
ERROR: Atom 767 velocity is 17521.9 8392.52 13850.3 (limit is 12000, atom
36 of 2823 on patch 1 pe 7)
ERROR: Atom 768 velocity is 10962.5 668.014 21254.4 (limit is 12000, atom
37 of 2823 on patch 1 pe 7)
ERROR: Atom 771 velocity is -19043.3 -6667.23 -31071.7 (limit is 12000,
atom 40 of 2823 on patch 1 pe 7)
ERROR: Atom 772 velocity is -17682.8 -3814.76 -25974.7 (limit is 12000,
atom 41 of 2823 on patch 1 pe 7)
ERROR: Atom 765 velocity is 7266.66 9867.88 -1673.52 (limit is 12000, atom
2606 of 2823 on patch 1 pe 7)
ERROR: Atoms moving too fast; simulation has become unstable (10 atoms on
patch 1 pe 7).
ERROR: Atom 729 velocity is -70110.3 -59189.4 -43414.8 (limit is 12000,
atom 2069 of 2599 on patch 7 pe 7)
ERROR: Atom 730 velocity is 10967.8 -12286 4416.83 (limit is 12000, atom
2070 of 2599 on patch 7 pe 7)
ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on
patch 7 pe 7).
ERROR: Atom 591 velocity is 10744.2 -5565.32 20901.3 (limit is 12000, atom
11 of 2861 on patch 14 pe 9)
ERROR: Atom 603 velocity is -7786.89 5356.79 -17338.7 (limit is 12000, atom
19 of 2861 on patch 14 pe 9)
ERROR: Atom 604 velocity is -122039 62193 -230801 (limit is 12000, atom 20
of 2861 on patch 14 pe 9)
ERROR: Atoms moving too fast; simulation has become unstable (3 atoms on
patch 14 pe 9).
ERROR: Atom 10 velocity is -8425.28 -12856.3 5722.31 (limit is 12000, atom
8 of 2838 on patch 3 pe 3)
ERROR: Atom 245 velocity is -55510.8 10925.4 23623.5 (limit is 12000, atom
2606 of 2838 on patch 3 pe 3)
ERROR: Atom 246 velocity is -52936.6 13725.5 24330.1 (limit is 12000, atom
2607 of 2838 on patch 3 pe 3)
ERROR: Atom 248 velocity is 36347.1 -6512.12 -15728.4 (limit is 12000, atom
2754 of 2838 on patch 3 pe 3)
ERROR: Atom 249 velocity is 35505.3 -9108.13 -14399.2 (limit is 12000, atom
2755 of 2838 on patch 3 pe 3)
ERROR: Atom 250 velocity is 36453.7 -9971.88 -16954.6 (limit is 12000, atom
2756 of 2838 on patch 3 pe 3)
ERROR: Atoms moving too fast; simulation has become unstable (6 atoms on
patch 3 pe 3).
[Partition 0][Node 0] End of program
any help will be appreciated.
Regards,
Farideh
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