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[08:17:28] Folding@Home Gromacs SMP Core
[08:17:28] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[08:17:28]
[08:17:28] Preparing to commence simulation
[08:17:28] - Ensuring status. Please wait.
[08:17:37] - Looking at optimizations...
[08:17:37] - Working with standard loops on this execution.
[08:17:37] - Files status OK
[08:17:38] - Expanded 4836004 -> 24036661 (decompressed 497.0 percent)
[08:17:38] Called DecompressByteArray: compressed_data_size=4836004 data_size=24036661, decompressed_data_size=24036661 diff=0
[08:17:39] - Digital signature verified
[08:17:39]
[08:17:39] Project: 2671 (Run 49, Clone 67, Gen 13)
[08:17:39]
[08:17:39] Entering M.D.
[08:17:45] Using Gromacs checkpoints
NNODES=8, MYRANK=0, HOSTNAME=Endeavour
NNODES=8, MYRANK=3, HOSTNAME=Endeavour
NNODES=8, MYRANK=1, HOSTNAME=Endeavour
NNODES=8, MYRANK=5, HOSTNAME=Endeavour
NNODES=8, MYRANK=7, HOSTNAME=Endeavour
NNODES=8, MYRANK=2, HOSTNAME=Endeavour
NNODES=8, MYRANK=4, HOSTNAME=Endeavour
NNODES=8, MYRANK=6, HOSTNAME=Endeavour
NODEID=0 argc=23
NODEID=1 argc=23
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.99_development_20090307 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
:-) mdrun (-:
Reading file work/wudata_03.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=6 argc=23
NODEID=4 argc=23
NODEID=5 argc=23
NODEID=2 argc=23
NODEID=3 argc=23
NODEID=7 argc=23
Note: tpx file_version 48, software version 64
Reading checkpoint file work/wudata_03.cpt generated: Tue May 5 02:27:30 2009
NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance create a new tpr file with an up to date version of grompp
Making 3D domain decomposition 2 x 2 x 2
starting mdrun '22866 system in water'
3500000 steps, 7000.0 ps (continuing from step 3250010, 6500.0 ps).
[08:17:47] Resuming from checkpoint
[08:17:47] Verified work/wudata_03.log
[08:17:47] Verified work/wudata_03.trr
[08:17:47] Verified work/wudata_03.xtc
[08:17:47] Verified work/wudata_03.edr
[08:17:47] Completed 10 out of 250000 steps (0%)
Step 3250042, time 6500.08 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005049, max 0.153571 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12377 12379 90.0 0.1090 0.1257 0.1090
12380 12382 90.0 0.1090 0.1243 0.1090
Step 3250043, time 6500.09 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001567, max 0.062674 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12377 12379 90.0 0.1257 0.1158 0.1090
Step 3250044, time 6500.09 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004545, max 0.145226 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12377 12379 90.0 0.1158 0.1248 0.1090
12380 12382 90.0 0.1089 0.1217 0.1090
Step 3250045, time 6500.09 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 3.120422, max 111.609711 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12380 12381 90.0 0.1110 0.9189 0.1090
Warning: 1-4 interaction between 12382 and 12384 at distance 27.450 which is larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 3250046, time 6500.09 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 38.075437, max 1283.494141 (between atoms 14123 and 14125)
Step 3250046, time 6500.09 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 95.171961, max 3921.419434 (between atoms 12380 and 12381)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12377 12379 90.0 12.2745 10.6873 0.1090
12380 12381 90.0 0.9189 427.5437 0.1090
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
14123 14124 90.0 0.1090 2.6297 0.1090
14123 14126 90.0 0.1090 2.4497 0.1090
Warning: 1-4 interaction between 14119 and 14125 at distance 160.427 which is larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 3250047, time 6500.09 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 4605097220767744.000000 (between atoms 14123 and 14125)
Step 3250047, time 6500.09 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 398105870336.000000 (between atoms 21729 and 21730)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
21755 21756 90.0 0.1090 841.8890 0.1090
21755 21757 90.1 0.1090 15891.9805 0.1090
21758 21760 90.0 0.1090 0.3193 0.1090
21731 21732 90.0 0.1090 1948560768.0000 0.1090
21731 21733 90.0 0.1090 19351518.0000 0.1090
Step 3250047, time 6500.09 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 129.047577 (between atoms 13523 and 13524)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
13521 13522 90.0 0.1010 0.6434 0.1010
13523 13524 90.0 2.3020 14.1752 0.1090
13525 13526 90.0 0.1090 0.6757 0.1090
12383 12385 90.0 0.1010 1.6799 0.1010
12374 12375 90.0 0.1090 0.2099 0.1090
t = 6500.094 ps: Water molecule starting at atom 29074 can not be settled.
Check for bad contacts and/or reduce the timestep.
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
12539 12540 90.0 0.1090 6934143.5000 0.1090
12541 12542 90.0 0.1090 351.9119 0.1090
12541 12543 91.8 0.1090 523.1652 0.1090
12541 12544 90.0 0.1090 522.4516 0.1090
12545 12546 90.0 0.1090 672605568.0000 0.1090
12545 12547 90.0 0.1090 670442240.0000 0.1090
8093 8096 90.0 0.1090 0.2780 0.1090
8097 8098 91.3 0.1090 708.4280 0.1090
8100 8101 98.1 0.1090 55.9082 0.1090
8100 8102 90.0 0.1090 3.1610 0.1090
8100 8103 90.0 0.1090 5.8512 0.1090
12504 12505 90.3 0.1090 2888.2185 0.1090
8087 8088 90.0 0.1010 0.1248 0.1010
8119 8121 92.5 0.1090 332.4854 0.1090
8119 8122 122.5 0.1090 5.1981 0.1090
12497 12498 90.0 0.1010 4367650914304.0000 0.1010
12499 12500 90.0 0.1090 219119091712.0000 0.1090
12501 12502 90.0 0.1090 8.7054 0.1090
12501 12503 90.0 0.1090 198.0699 0.1090
Step 3250047, time 6500.09 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1610.863821, max 98658.015625 (between atoms 14146 and 14147)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
14133 14134 90.0 0.1090 8697.7539 0.1090
14133 14135 90.1 0.1090 10984.3486 0.1090
14144 14145 91.7 0.1010 1087.5610 0.1010
14182 14183 90.0 0.1010 812602.8125 0.1010
14184 14185 90.0 0.1090 1103690203136.0000 0.1090
14192 14193 90.0 0.1090 290097.7188 0.1090
14192 14194 90.0 0.1090 191953.4531 0.1090
14192 14195 90.0 0.1090 289900.7188 0.1090
12506 12507 90.1 0.1090 6482.4897 0.1090
14123 14125 90.0 140.0099 501955579346944.0000 0.1090
14136 14137 90.0 0.1090 55939944448.0000 0.1090
12450 12451 90.0 0.1090 3561.5610 0.1090
12452 12453 130.4 0.1090 7.8651 0.1090
12452 12454 97.9 0.1090 97.9999 0.1090
14086 14087 90.0 0.1090 0.1270 0.1090
t = 6500.094 ps: Water molecule starting at atom 139786 can not be settled.
Check for bad contacts and/or reduce the timestep.
[08:18:28] ***** Got an Activate signal (2)
[08:18:28] Killing all core threads
Folding@Home Client Shutdown.