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
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