add dihedral parameter for you EPON molecule. Check this:
http://oldwww.gromacs.org/pipermail/gmx-users/2005-May/015044.html 2010/10/24 英雄不再寂寞 <xiaowu...@qq.com> > Dear gmxers, > I try to simulate a complex system using gmx-4.5.1. I have carried out > the minimization without any errors, but when it comes to molecular > dynamics, some errors are printed and given below. How to deal with this > problem? Please give me some hints. Thanks a lot for any reply. > > Yours sincerely, > Chaofu Wu, Dr. > > xiaowu...@linux-s38y:~/workshop> mdrun -s detamix_md01.tpr -o > detamix_md01.trr -c detamix_md01.gro -e detamix_md01.edr -g detamix_md01.log > -v -np 4 -N 4 > :-) G R O M A C S (-: > GROup of MAchos and Cynical Suckers > :-) VERSION 4.5.1 (-: > Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, > Aldert van Buuren, P盲r Bjelkmar, Rudi van Drunen, Anton Feenstra, > Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff, > Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz, > 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 > ------------------------------------------------------------ > ...... > Option Type Value Description > ------------------------------------------------------ > ...... > Getting Loaded... > Reading file detamix_md01.tpr, VERSION 4.5.1 (single precision) > Starting 4 threads > Loaded with Money > > NOTE: Periodic molecules: can not easily determine the required minimum > bonded cut-off, using half the non-bonded cut-off > Making 1D domain decomposition 4 x 1 x 1 > starting mdrun '40 deta + 100 epon862 + 1 SWCNT(10,10)' > 4000000 steps, 4000.0 ps. > step 0 > NOTE: Turning on dynamic load balancing > step 39500, will finish Mon Oct 25 02:51:47 2010vol 0.61 imb F 14% > A list of missing interactions: > Ryckaert-Bell. of 12880 missing 2 > Molecule type 'EPON' > the first 10 missing interactions, except for exclusions: > Ryckaert-Bell. atoms 11 12 14 16 global 5481 5482 5484 > 5486 > Ryckaert-Bell. atoms 16 21 23 11 global 5486 5491 5493 > 5481 > ------------------------------------------------------- > Program mdrun, VERSION 4.5.1 > Source code file: domdec_top.c, line: 356 > Fatal error: > 2 of the 79000 bonded interactions could not be calculated because some > atoms involved moved further apart than the multi-body cut-off distance (0.5 > nm) or the two-body cut-off distance (1 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 > ------------------------------------------------------- > "Jede der Scherben spiegelt das Licht" (Wir sind Helden) > xiaowu...@linux-s38y:~/workshop> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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