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

Jindao zhangjd09 at lzu.cn
Mon Oct 25 06:03:39 CEST 2010 

2010/10/25 英雄不再寂寞 <xiaowu759 at qq.com>

> 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.
>  ------------------ 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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Before normal md, you can try mainchain constrain md, Good luck

-- 
kyz00  ------
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