Re: [votca] error in gromacs while performing mdrun -deffnm nvt
Victor Ruehle
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 <gaur...@gmail.com>:
> 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 vo...@googlegroups.com.
> To unsubscribe from this group, send email to votca+un...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/votca?hl=en.
>
>
