Dear all, I´m getting the same error. Did you finaly find the problem?
Javier On Wednesday, April 20, 2011 at 3:49:06 AM UTC-5, Victor Ruehle wrote: > > Hey, > > seems like a gromacs problem, is this problem somehow related to > votca? If not, please ask at the gromacs mailing list. > > http://www.gromacs.org/Support/Mailing_Lists > > Victor > > 2011/4/20 gauri <[email protected] <javascript:>>: > > the following is ma result when i entered the command mdrun - > > deffnm nvt > > > > > > > > > > [root@localhost gromacs-4.5.3]# mdrun -deffnm nvt > > :-) G R O M A C S (-: > > > > GRoups of Organic Molecules in ACtion for Science > > > > :-) VERSION 4.5.3 (-: > > > > Written by Emile Apol, Rossen Apostolov, Herman J.C. > > Berendsen, > > Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton > > Feenstra, > > Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter > > Meulenhoff, > > Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, > > Michael Shirts, Alfons Sijbers, Peter Tieleman, > > > > Berk Hess, David van der Spoel, and Erik Lindahl. > > > > Copyright (c) 1991-2000, University of Groningen, The > > Netherlands. > > Copyright (c) 2001-2010, The GROMACS development team at > > Uppsala University & The Royal Institute of Technology, > > Sweden. > > 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 (-: > > > > Option Filename Type Description > > ------------------------------------------------------------ > > -s nvt.tpr Input Run input file: tpr tpb tpa > > -o nvt.trr Output Full precision trajectory: trr trj > > cpt > > -x nvt.xtc Output, Opt. Compressed trajectory (portable xdr > > format) > > -cpi nvt.cpt Input, Opt. Checkpoint file > > -cpo nvt.cpt Output, Opt. Checkpoint file > > -c nvt.gro Output Structure file: gro g96 pdb etc. > > -e nvt.edr Output Energy file > > -g nvt.log Output Log file > > -dhdl nvt.xvg Output, Opt. xvgr/xmgr file > > -field nvt.xvg Output, Opt. xvgr/xmgr file > > -table nvt.xvg Input, Opt. xvgr/xmgr file > > -tablep nvt.xvg Input, Opt. xvgr/xmgr file > > -tableb nvt.xvg Input, Opt. xvgr/xmgr file > > -rerun nvt.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb > > cpt > > -tpi nvt.xvg Output, Opt. xvgr/xmgr file > > -tpid nvt.xvg Output, Opt. xvgr/xmgr file > > -ei nvt.edi Input, Opt. ED sampling input > > -eo nvt.edo Output, Opt. ED sampling output > > -j nvt.gct Input, Opt. General coupling stuff > > -jo nvt.gct Output, Opt. General coupling stuff > > -ffout nvt.xvg Output, Opt. xvgr/xmgr file > > -devout nvt.xvg Output, Opt. xvgr/xmgr file > > -runav nvt.xvg Output, Opt. xvgr/xmgr file > > -px nvt.xvg Output, Opt. xvgr/xmgr file > > -pf nvt.xvg Output, Opt. xvgr/xmgr file > > -mtx nvt.mtx Output, Opt. Hessian matrix > > -dn nvt.ndx Output, Opt. Index file > > > > Option Type Value Description > > ------------------------------------------------------ > > -[no]h bool no Print help info and quit > > -[no]version bool no Print version info and quit > > -nice int 0 Set the nicelevel > > -deffnm string nvt Set the default filename for all file > > options > > -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or > > none > > -[no]pd bool no Use particle decompostion > > -dd vector 0 0 0 Domain decomposition grid, 0 is optimize > > -nt int 0 Number of threads to start (0 is guess) > > -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 > > -gcom int -1 Global communication frequency > > -[no]v bool no 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]cpnum bool no Keep and number checkpoint files > > -[no]append bool yes Append to previous output files when > > continuing > > from checkpoint instead of adding the > > simulation > > part number to all file names > > -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]ionize bool no Do a simulation including the effect of an > > X-Ray > > bombardment on your system > > > > > > Back Off! I just backed up nvt.log to ./#nvt.log.6# > > Reading file nvt.tpr, VERSION 4.5.3 (single precision) > > > > Back Off! I just backed up nvt.trr to ./#nvt.trr.6# > > > > Back Off! I just backed up nvt.edr to ./#nvt.edr.6# > > starting mdrun 'Protein in water' > > 5000 steps, 10.0 ps. > > > > Step 0, time 0 (ps) LINCS WARNING > > relative constraint deviation after LINCS: > > rms 254.970621, max 23208.900391 (between atoms 412 and 413) > > bonds that rotated more than 30 degrees: > > atom 1 atom 2 angle previous, current, constraint length > > 6387 6388 90.0 0.1090 0.1555 0.1090 > > 4436 4437 90.1 0.1090 0.1236 0.1090 > > 4324 4325 90.0 0.1090 0.7974 0.1090 > > 4303 4304 90.1 0.1090 0.1417 0.1090 > > 4226 4227 63.0 0.1090 0.1096 0.1090 > > 3761 3762 90.4 0.1080 0.3299 0.1080 > > 3255 3257 35.0 0.1343 0.1358 0.1343 > > 3255 3256 90.0 0.1080 3.7774 0.1080 > > 3253 3254 90.4 0.1080 0.1175 0.1080 > > 3252 3255 35.8 0.1335 0.1372 0.1335 > > 3158 3159 90.0 0.1090 0.1430 0.1090 > > 2981 2982 39.3 0.1090 0.1092 0.1090 > > 2622 2624 90.0 0.1090 0.2783 0.1090 > > 2135 2136 90.0 0.1090 0.1386 0.1090 > > 453 455 36.4 0.1449 0.1940 0.1449 > > 453 454 43.6 0.1010 0.1519 0.1010 > > 451 453 124.0 0.1335 0.1858 0.1335 > > 451 452 118.9 0.1229 0.2184 0.1229 > > 436 439 35.5 0.1529 0.1909 0.1529 > > 436 438 42.4 0.1090 0.1509 0.1090 > > 436 437 41.7 0.1090 0.1491 0.1090 > > 433 436 135.1 0.1529 0.1449 0.1529 > > 433 435 115.3 0.1090 0.1940 0.1090 > > 433 434 117.1 0.1090 0.1943 0.1090 > > 431 451 101.0 0.1522 2.3397 0.1522 > > 431 433 101.8 0.1529 2.2716 0.1529 > > 431 432 102.5 0.1090 2.3463 0.1090 > > 429 431 101.9 0.1449 8.9042 0.1449 > > 429 430 102.0 0.1010 8.0492 0.1010 > > 427 429 98.5 0.1335 26.3947 0.1335 > > 427 428 98.3 0.1229 24.7635 0.1229 > > 423 426 100.5 0.1090 1.3891 0.1090 > > 423 425 99.8 0.1090 1.3961 0.1090 > > 423 424 99.8 0.1090 1.3968 0.1090 > > 419 422 94.0 0.1090 8.5287 0.1090 > > 419 421 95.1 0.1090 7.2151 0.1090 > > 419 420 95.2 0.1090 7.1888 0.1090 > > 416 423 96.9 0.1529 7.2402 0.1529 > > 416 418 96.2 0.1090 7.0079 0.1090 > > 416 417 96.5 0.1090 6.9782 0.1090 > > 414 419 93.5 0.1529 32.3572 0.1529 > > 414 416 93.7 0.1529 33.5792 0.1529 > > 414 415 93.8 0.1090 29.8089 0.1090 > > 412 427 92.8 0.1522 104.5719 0.1522 > > 412 414 92.3 0.1529 96.8648 0.1529 > > 412 413 90.1 0.1090 2529.8792 0.1090 > > 410 412 92.3 0.1449 97.4995 0.1449 > > 410 411 95.1 0.1010 23.6972 0.1010 > > 408 410 95.4 0.1335 27.9529 0.1335 > > 408 409 103.3 0.1229 7.9893 0.1229 > > 404 407 48.8 0.1090 0.1697 0.1090 > > 404 406 48.8 0.1090 0.1695 0.1090 > > 404 405 49.2 0.1090 0.1709 0.1090 > > 400 403 49.6 0.1090 0.1723 0.1090 > > 400 402 49.2 0.1090 0.1712 0.1090 > > 400 401 49.6 0.1090 0.1699 0.1090 > > 398 404 118.9 0.1529 0.2370 0.1529 > > 398 400 118.7 0.1529 0.2396 0.1529 > > 398 399 109.4 0.1090 0.2621 0.1090 > > 396 408 105.2 0.1522 7.8556 0.1522 > > 396 398 102.3 0.1529 2.3503 0.1529 > > 396 397 102.2 0.1090 2.4204 0.1090 > > 394 396 101.0 0.1449 2.3903 0.1449 > > 394 395 117.4 0.1010 0.2084 0.1010 > > 392 394 149.0 0.1335 0.1589 0.1335 > > 392 393 33.0 0.1229 0.1588 0.1229 > > 354 355 90.0 0.1090 1.9108 0.1090 > > 319 321 90.0 0.1090 0.5796 0.1090 > > 319 320 34.1 0.1090 0.1097 0.1090 > > 194 195 52.0 0.1090 0.1092 0.1090 > > 149 150 46.0 0.1090 0.1088 0.1090 > > 107 110 82.2 0.1529 0.1990 0.1529 > > 107 109 90.0 0.1090 0.6371 0.1090 > > 107 108 90.0 0.1090 0.2027 0.1090 > > 105 107 76.8 0.1529 0.2081 0.1529 > > 43 44 90.0 0.1090 0.1685 0.1090 > > > > step 0: Water molecule starting at atom 41635 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > > > Back Off! I just backed up step0b.pdb to ./#step0b.pdb.6# > > > > Back Off! I just backed up step0c.pdb to ./#step0c.pdb.6# > > Wrote pdb files with previous and current coordinates > > Segmentation fault > > > > > > > > > > > > > > > > > > please help me out > > > > -- > > You received this message because you are subscribed to the Google > Groups "votca" group. > > To post to this group, send email to [email protected] > <javascript:>. > > To unsubscribe from this group, send email to > [email protected] <javascript:>. > > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > > > > > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
