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

[Justin A. Lemkul]

英雄不再寂寞 wrote:
> 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.

Sounds like it could be a topology issue.  Some tips are here:

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

-Justin

> Yours sincerely,
> Chaofu Wu, Dr.
> ------------------ 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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-- 
========================================

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

========================================