Project: 6901 (Run 10, Clone 17, Gen 123)
Posted: Thu Oct 27, 2011 1:16 pm
Problem with this wu.. here the log
Code: Select all
[23:04:31] Project: 6901 (Run 10, Clone 17, Gen 123)
[23:04:31]
[23:04:31] Entering M.D.
[23:04:38] Using Gromacs checkpoints
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) 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.
:-) Gromacs (-:
[23:04:42] Mapping NT from 16 to 16
Reading file work/wudata_05.tpr, VERSION 4.0.99_development_20090605 (single precision)
Note: tpx file_version 70, software version 73
Starting 16 threads
Reading checkpoint file work/wudata_05.cpt generated: Wed Oct 26 03:09:41 2011
Making 2D domain decomposition 4 x 4 x 1
starting mdrun 'SINGLE VESICLE in water'
31000000 steps, 124000.0 ps (continuing from step 30793315, 123173.3 ps).
;[23:05:02] Resuming from checkpoint
[23:05:07] Verified work/wudata_05.log
[23:05:07] Verified work/wudata_05.trr
[23:05:07] Verified work/wudata_05.xtc
[23:05:07] Verified work/wudata_05.edr
[23:05:08] Completed 43315 out of 250000 steps (17%)
[23:19:13] Completed 45000 out of 250000 steps (18%)
[23:40:09] Completed 47500 out of 250000 steps (19%)
[00:01:07] Completed 50000 out of 250000 steps (20%)
[00:22:04] Completed 52500 out of 250000 steps (21%)
[00:42:59] Completed 55000 out of 250000 steps (22%)
[01:03:54] Completed 57500 out of 250000 steps (23%)
[01:24:49] Completed 60000 out of 250000 steps (24%)
[01:45:49] Completed 62500 out of 250000 steps (25%)
[02:06:44] Completed 65000 out of 250000 steps (26%)
[02:27:37] Completed 67500 out of 250000 steps (27%)
[02:48:33] Completed 70000 out of 250000 steps (28%)
[03:09:34] Completed 72500 out of 250000 steps (29%)
[03:30:31] Completed 75000 out of 250000 steps (30%)
[03:51:26] Completed 77500 out of 250000 steps (31%)
[04:12:20] Completed 80000 out of 250000 steps (32%)
[04:33:14] Completed 82500 out of 250000 steps (33%)
[04:54:11] Completed 85000 out of 250000 steps (34%)
[05:04:18] - Autosending finished units... [October 27 05:04:18 UTC]
[05:04:18] Trying to send all finished work units
[05:04:18] + No unsent completed units remaining.
[05:04:18] - Autosend completed
[05:15:08] Completed 87500 out of 250000 steps (35%)
[05:36:01] Completed 90000 out of 250000 steps (36%)
A list of missing interactions:
exclusions of 1292913 missing 125393
-------------------------------------------------------
Program Gromacs, VERSION 4.5.3
Source code file: /vspm58/VM/fah-converted/mnt/fah_windows_build/LinuxBuilds/gromacs-4.5.3/src/mdlib/domdec_top.c, line: 356
Fatal error:
125393 of the 1925552 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
[05:49:38] mdrun returned 255
[05:49:38] Going to send back what have done -- stepsTotalG=250000
[05:49:38] Work fraction=335.7793 steps=250000.
[05:49:42] logfile size=81646 infoLength=81646 edr=25 trr=1
[05:49:42] logfile size: 81646 info=81646 bed=25 hdr=1
[05:49:42] - Writing 82184 bytes of core data to disk...
[05:49:42] ... Done.