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

[英雄不再寂寞]

Dear gmxers,
   The problem continues to puzzle me. I realize that only the EPON molecules with two phenyls lead to the problem. Then, may it be due to the ring catenations in the structure? Please give me some hints. Thanks a lot.
 Yours sincerely,
 Chaofu Wu, Dr.</:includetail>
  ------------------ 原始邮件 ------------------
  发件人: "Justin A. Lemkul"<jalemkul at vt.edu>;
 发送时间: 2010年10月24日(星期天) 上午8:20
 收件人: "Discussion list for GROMACS users"<gmx-users at gromacs.org>; 
 
 主题: Re: [gmx-users] the first 10 missing interactions,except for exclusions...

  
 

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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</:includetail>
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