[gmx-users] the first 10 missing interactions, except for exclusions...

[Justin A. Lemkul]

英雄不再寂寞 wrote:
> 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.
>  
> xiaowu759 at linux-s38y:~/workshop 
> <mailto:xiaowu759 at 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)
> xiaowu759 at linux-s38y:~/workshop <mailto:xiaowu759 at linux-s38y:~/workshop>>
>  
> 

Sounds like your system is blowing up.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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