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bbslover金虫 (正式写手)
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mpirun -np 8 mdrun_mpi -v -s 这步出错
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我下载了一个蛋白，有4条链A B C D。是对称的，我删除了B C D链，剩下A链用来做对接。对接结束后，观察对接结果还算满意，和晶体结构的结合模式差不多。 然后我用dock之后的配体和蛋白的complex来跑MD （使用gromacs），之前的步骤都是正确的，但是，当输入命令：mpirun -np 8 mdrun_mpi -v -s pr_m027.tpr -o pr_m027.trr -c m027_after_pr.gro -e pr_m027.edr -g m027_pr.log 之后，就出错了，错误如下，希望大家帮忙看一下吧，谢谢，我该如何解决呢？ NNODES=8, MYRANK=0, HOSTNAME=localhost.localdomain NNODES=8, MYRANK=3, HOSTNAME=localhost.localdomain NNODES=8, MYRANK=2, HOSTNAME=localhost.localdomain NNODES=8, MYRANK=5, HOSTNAME=localhost.localdomain NNODES=8, MYRANK=6, HOSTNAME=localhost.localdomain NNODES=8, MYRANK=4, HOSTNAME=localhost.localdomain NNODES=8, MYRANK=1, HOSTNAME=localhost.localdomain NNODES=8, MYRANK=7, HOSTNAME=localhost.localdomain NODEID=3 argc=12 NODEID=7 argc=12 NODEID=4 argc=12 NODEID=1 argc=12 NODEID=0 argc=12 :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 4.0.5 (-: 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. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun_mpi (-: Option Filename Type Description ------------------------------------------------------------ -s pr_m027.tpr Input Run input file: tpr tpb tpa -o pr_m027.trr Output Full precision trNODEID=2 argc=12 NODEID=6 argc=12 NODEID=5 argc=12 ajectory: trr trj cpt -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi state.cpt Input, Opt. Checkpoint file -cpo state.cpt Output, Opt. Checkpoint file -c m027_after_pr.gro Output Structure file: gro g96 pdb -e pr_m027.edr Output Energy file: edr ene -g m027_pr.log Output Log file -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file -field field.xvg Output, Opt. xvgr/xmgr file -table table.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file -tableb table.xvg Input, Opt. xvgr/xmgr file -rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi tpi.xvg Output, Opt. xvgr/xmgr file -tpid tpidist.xvg Output, Opt. xvgr/xmgr file -ei sam.edi Input, Opt. ED sampling input -eo sam.edo Output, Opt. ED sampling output -j wham.gct Input, Opt. General coupling stuff -jo bam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file -px pullx.xvg Output, Opt. xvgr/xmgr file -pf pullf.xvg Output, Opt. xvgr/xmgr file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -deffnm string Set the default filename for all file options -[no]xvgr bool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -npme int -1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum auto Dynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -[no]sum bool yes Sum the energies at every step -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -pforce real -1 Print all forces larger than this (kJ/mol nm) -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility -cpt real 15 Checkpoint interval (minutes) -[no]append bool no Append to previous output files when continuing from checkpoint -[no]addpart bool yes Add the simulation part number to all output files when continuing from checkpoint -maxh real -1 Terminate after 0.99 times this time (hours) -multi int 0 Do multiple simulations in parallel -replex int 0 Attempt replica exchange every # steps -reseed int -1 Seed for replica exchange, -1 is generate a seed -[no]glas bool no Do glass simulation with special long range corrections -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system Getting Loaded... Reading file pr_m027.tpr, VERSION 4.0.5 (single precision) Loaded with Money Making 1D domain decomposition 8 x 1 x 1 starting mdrun 'Protein in water' 100000 steps, 200.0 ps. step 0 imb F 4% step 100, will finish Tue Sep 6 09:24:47 2011 imb F 3% step 200, will finish Tue Sep 6 09:16:59 2011 imb F 4% step 300, will finish Tue Sep 6 09:19:54 2011 imb F 4% step 400, will finish Tue Sep 6 09:17:13 2011 imb F 4% step 500, will finish Tue Sep 6 09:15:36 2011 imb F 3% step 600, will finish Tue Sep 6 09:14:31 2011 imb F 3% step 700, will finish Tue Sep 6 09:13:45 2011 imb F 4% step 800, will finish Tue Sep 6 09:13:10 2011 imb F 4% step 900, will finish Tue Sep 6 09:12:43 2011 imb F 4% step 1000, will finish Tue Sep 6 09:14:01 2011 imb F 4% step 1100, will finish Tue Sep 6 09:13:34 2011 imb F 4% step 1200, will finish Tue Sep 6 09:13:12 2011 imb F 4% step 1300, will finish Tue Sep 6 09:12:53 2011 imb F 4% step 1400, will finish Tue Sep 6 09:12:37 2011 imb F 4% step 1500, will finish Tue Sep 6 09:12:23 2011 imb F 4% step 1600, will finish Tue Sep 6 09:12:11 2011 imb F 4% step 1700, will finish Tue Sep 6 09:12:00 2011 imb F 4% step 1800, will finish Tue Sep 6 09:11:50 2011 imb F 4% step 1900, will finish Tue Sep 6 09:11:42 2011 imb F 5% step 2000, will finish Tue Sep 6 09:11:34 2011 imb F 5% step 2100, will finish Tue Sep 6 09:11:27 2011 imb F 4% step 2200, will finish Tue Sep 6 09:11:21 2011 imb F 3% step 2300, will finish Tue Sep 6 09:11:15 2011 imb F 3% step 2400, will finish Tue Sep 6 09:11:09 2011 imb F 2% step 2500, will finish Tue Sep 6 09:11:05 2011 imb F 2% step 2600, will finish Tue Sep 6 09:11:00 2011 imb F 4% step 2700, will finish Tue Sep 6 09:10:56 2011 imb F 3% step 2800, will finish Tue Sep 6 09:10:52 2011 imb F 2% step 2900, will finish Tue Sep 6 09:10:14 2011 imb F 2% step 3000, will finish Tue Sep 6 09:10:12 2011 imb F 3% step 3100, will finish Tue Sep 6 09:10:09 2011 imb F 4% step 3200, will finish Tue Sep 6 09:10:07 2011 imb F 2% step 3300, will finish Tue Sep 6 09:10:06 2011 Step 3378, time 6.756 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000107, max 0.002371 (between atoms 3110 and 3108) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3110 3108 32.5 0.0998 0.0998 0.1000 Step 3386, time 6.772 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000114, max 0.001512 (between atoms 3110 and 3108) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3110 3108 30.7 0.1002 0.1002 0.1000 imb F 2% step 3400, will finish Tue Sep 6 09:10:04 2011 Step 3422, time 6.844 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000056, max 0.000864 (between atoms 3110 and 3108) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3109 3108 30.7 0.0997 0.1001 0.1000 imb F 1% step 3500, will finish Tue Sep 6 09:10:02 2011 Step 3504, time 7.008 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000148, max 0.001221 (between atoms 3110 and 3108) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3110 3108 30.2 0.1003 0.1001 0.1000 imb F 2% step 3600, will finish Tue Sep 6 09:09:33 2011 Step 3622, time 7.244 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000118, max 0.001028 (between atoms 3113 and 3112) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3110 3108 30.5 0.1002 0.0999 0.1000 imb F 1% step 3700, will finish Tue Sep 6 09:09:32 2011 imb F 2% step 3800, will finish Tue Sep 6 09:09:32 2011 imb F 3% step 3900, will finish Tue Sep 6 09:09:31 2011 imb F 2% step 4000, will finish Tue Sep 6 09:09:30 2011 imb F 2% step 4100, will finish Tue Sep 6 09:09:30 2011 imb F 2% step 4200, will finish Tue Sep 6 09:09:29 2011 imb F 2% step 4300, will finish Tue Sep 6 09:09:29 2011 imb F 2% step 4400, will finish Tue Sep 6 09:09:05 2011 Step 4417, time 8.834 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000067, max 0.001497 (between atoms 3110 and 3108) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3110 3108 30.2 0.0998 0.1001 0.1000 Step 4418, time 8.836 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000079, max 0.001814 (between atoms 3110 and 3108) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3110 3108 34.1 0.1000 0.0998 0.1000 Step 4419, time 8.838 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000100, max 0.002377 (between atoms 3110 and 3108) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3110 3108 31.2 0.0997 0.0998 0.1000 Step 4430, time 8.86 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000107, max 0.001366 (between atoms 3109 and 3108) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3109 3108 31.3 0.1001 0.0999 0.1000 imb F 2% step 4500, will finish Tue Sep 6 09:09:05 2011 imb F 2% step 4600, will finish Tue Sep 6 09:09:05 2011 imb F 2% step 4700, will finish Tue Sep 6 09:09:05 2011 imb F 3% step 4800, will finish Tue Sep 6 09:09:06 2011 imb F 3% step 4900, will finish Tue Sep 6 09:09:06 2011 imb F 2% step 5000, will finish Tue Sep 6 09:09:06 2011 imb F 2% step 5100, will finish Tue Sep 6 09:09:06 2011 imb F 2% step 5200, will finish Tue Sep 6 09:09:06 2011 imb F 2% step 5300, will finish Tue Sep 6 09:09:06 2011 imb F 1% step 5400, will finish Tue Sep 6 09:09:06 2011 imb F 2% step 5500, will finish Tue Sep 6 09:09:06 2011 imb F 2% step 5600, will finish Tue Sep 6 09:09:06 2011 imb F 2% step 5700, will finish Tue Sep 6 09:09:06 2011 imb F 2% step 5800, will finish Tue Sep 6 09:09:06 2011 imb F 1% step 5900, will finish Tue Sep 6 09:08:49 2011 imb F 1% step 6000, will finish Tue Sep 6 09:08:49 2011 imb F 1% step 6100, will finish Tue Sep 6 09:08:49 2011 imb F 3% step 6200, will finish Tue Sep 6 09:08:50 2011 imb F 3% step 6300, will finish Tue Sep 6 09:08:50 2011 imb F 3% step 6400, will finish Tue Sep 6 09:08:50 2011 imb F 2% step 6500, will finish Tue Sep 6 09:08:50 2011 imb F 2% step 6600, will finish Tue Sep 6 09:08:51 2011 imb F 2% step 6700, will finish Tue Sep 6 09:08:51 2011 imb F 3% step 6800, will finish Tue Sep 6 09:08:51 2011 imb F 4% step 6900, will finish Tue Sep 6 09:08:51 2011 imb F 4% step 7000, will finish Tue Sep 6 09:08:52 2011 imb F 4% step 7100, will finish Tue Sep 6 09:08:52 2011 imb F 4% step 7200, will finish Tue Sep 6 09:08:52 2011 imb F 4% step 7300, will finish Tue Sep 6 09:08:52 2011 imb F 3% step 7400, will finish Tue Sep 6 09:08:52 2011 imb F 3% step 7500, will finish Tue Sep 6 09:08:39 2011 imb F 4% step 7600, will finish Tue Sep 6 09:08:40 2011 Step 7608, time 15.216 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000086, max 0.001847 (between atoms 3110 and 3108) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3110 3108 31.7 0.1000 0.1002 0.1000 imb F 4% step 7700, will finish Tue Sep 6 09:08:40 2011 imb F 3% step 7800, will finish Tue Sep 6 09:08:40 2011 imb F 3% step 7900, will finish Tue Sep 6 09:08:41 2011 imb F 2% step 8000, will finish Tue Sep 6 09:08:41 2011 imb F 2% step 8100, will finish Tue Sep 6 09:08:41 2011 imb F 2% step 8200, will finish Tue Sep 6 09:08:42 2011 imb F 2% step 8300, will finish Tue Sep 6 09:08:42 2011 imb F 2% step 8400, will finish Tue Sep 6 09:08:42 2011 imb F 2% step 8500, will finish Tue Sep 6 09:08:42 2011 imb F 1% step 8600, will finish Tue Sep 6 09:08:43 2011 imb F 2% step 8700, will finish Tue Sep 6 09:08:31 2011 imb F 2% step 8800, will finish Tue Sep 6 09:08:32 2011 imb F 3% step 8900, will finish Tue Sep 6 09:08:32 2011 imb F 3% step 9000, will finish Tue Sep 6 09:08:33 2011 imb F 2% step 9100, will finish Tue Sep 6 09:08:33 2011 imb F 2% step 9200, will finish Tue Sep 6 09:08:33 2011 imb F 3% step 9300, will finish Tue Sep 6 09:08:34 2011 imb F 2% step 9400, will finish Tue Sep 6 09:08:34 2011 imb F 3% step 9500, will finish Tue Sep 6 09:08:34 2011 imb F 3% step 9600, will finish Tue Sep 6 09:08:35 2011 imb F 2% step 9700, will finish Tue Sep 6 09:08:35 2011 imb F 3% step 9800, will finish Tue Sep 6 09:08:25 2011 imb F 2% step 9900, will finish Tue Sep 6 09:08:26 2011 imb F 2% step 10000, will finish Tue Sep 6 09:08:26 2011 imb F 2% step 10100, will finish Tue Sep 6 09:08:26 2011 imb F 3% step 10200, will finish Tue Sep 6 09:08:27 2011 imb F 3% step 10300, will finish Tue Sep 6 09:08:27 2011 imb F 3% step 10400, will finish Tue Sep 6 09:08:28 2011 imb F 3% step 10500, will finish Tue Sep 6 09:08:28 2011 imb F 3% step 10600, will finish Tue Sep 6 09:08:28 2011 imb F 2% step 10700, will finish Tue Sep 6 09:08:29 2011 imb F 3% step 10800, will finish Tue Sep 6 09:08:29 2011 imb F 2% step 10900, will finish Tue Sep 6 09:08:29 2011 Step 10982, time 21.964 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000136, max 0.002613 (between atoms 3103 and 3102) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 32.6 0.1091 0.1093 0.1090 Step 10983, time 21.966 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000181, max 0.003381 (between atoms 3103 and 3102) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 34.6 0.1093 0.1094 0.1090 Step 10984, time 21.968 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000143, max 0.001925 (between atoms 3112 and 3105) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 34.3 0.1094 0.1090 0.1090 Step 10985, time 21.97 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000142, max 0.002547 (between atoms 3103 and 3102) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 31.6 0.1090 0.1087 0.1090 Step 10989, time 21.978 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000099, max 0.000947 (between atoms 3103 and 3102) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 30.3 0.1092 0.1091 0.1090 Step 10990, time 21.98 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000128, max 0.001729 (between atoms 3103 and 3102) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 34.7 0.1093 0.1092 0.1090 Step 10991, time 21.982 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000123, max 0.001188 (between atoms 3101 and 3100) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 33.7 0.1094 0.1091 0.1090 imb F 7% step 11000, will finish Tue Sep 6 09:08:30 2011 Step 11011, time 22.022 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000077, max 0.000520 (between atoms 3112 and 3105) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3101 3100 30.0 0.1091 0.1090 0.1090 Step 11054, time 22.108 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000157, max 0.001518 (between atoms 3103 and 3102) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 30.1 0.1094 0.1092 0.1090 imb F 3% step 11100, will finish Tue Sep 6 09:08:30 2011 Step 11139, time 22.278 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000052, max 0.000629 (between atoms 3105 and 3104) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 31.8 0.1089 0.1090 0.1090 Step 11153, time 22.306 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000141, max 0.001937 (between atoms 3109 and 3108) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 31.9 0.1093 0.1091 0.1090 Step 11154, time 22.308 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000137, max 0.001428 (between atoms 3109 and 3108) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 33.9 0.1093 0.1090 0.1090 Step 11155, time 22.31 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000145, max 0.001613 (between atoms 3103 and 3102) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3103 3102 30.4 0.1092 0.1088 0.1090 Step 11157, time 22.314 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046125, max 0.919529 (between atoms 3103 and 3102) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3101 3100 89.9 0.1093 0.2071 0.1090 3103 3102 90.0 0.1092 0.2092 0.1090 Step 11158, time 22.316 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001070, max 0.025064 (between atoms 3103 and 3102) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3101 3100 48.3 0.2077 0.1077 0.1090 3103 3102 82.3 0.2098 0.1117 0.1090 Step 11159, time 22.318 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.033220, max 0.858396 (between atoms 3103 and 3102) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3101 3100 90.1 0.1080 0.1471 0.1090 3103 3102 90.0 0.1120 0.2026 0.1090 Step 11160, time 22.32 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1.377592, max 37.064606 (between atoms 3101 and 3100) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3105 3104 89.0 0.1333 0.7824 0.1330 3112 3105 86.1 0.1332 0.1472 0.1330 3106 3105 87.7 0.1333 0.1335 0.1330 3107 3106 33.1 0.1334 0.1410 0.1330 3100 3098 84.5 0.1329 0.5221 0.1330 3099 3098 84.5 0.1371 0.1425 0.1370 3104 3099 89.8 0.1373 0.8558 0.1370 3102 3100 91.6 0.1334 0.2853 0.1330 3101 3100 90.2 0.1475 4.1490 0.1090 3104 3102 89.8 0.1327 0.7938 0.1330 3103 3102 91.4 0.2031 0.5788 0.1090 Warning: 1-4 interaction between 3095 and 3101 at distance 4.237 which is larger than the 1-4 table size 2.400 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 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.0.5 Source code file: pme.c, line: 518 Fatal error: 1 particles communicated to PME node 2 are more than a cell length out of the domain decomposition cell of their charge group ------------------------------------------------------- "Jesus Can't Save You, Though It's Nice to Think He Tried" (Black Crowes) Error on node 2, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 2 out of 8 gcq#100: "Jesus Can't Save You, Though It's Nice to Think He Tried" (Black Crowes) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2 rank 2 in job 5 localhost.localdomain_36728 caused collective abort of all ranks exit status of rank 2: return code 255 |
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bbslover
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2楼2011-09-07 10:52:29