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

Fri Oct 29 10:33:06 CEST 2010

Dear Xiao and other gmxers,
   Thanks a lot for the reply. In fact, I also doubt that the top file causes the problem. In the EPON molecules, there are -CH2- group which are linked to two phenyl. In the parameter file of oplsaa force field, I can not find the suitable atom type for the C atoms. Instead, I had tried the opls_149 (CH3, toluene) or opls_148(CH2, ethyl benzene). One of possible solution to my problem can be creating new atom type for -CH2-, but it is very hard work to optimize the parameters. So, have you simulated/found such a similar molecule(there are -CH2- group which are linked to two phenyl) in the format of oplsaa force field? If yes, please kindly give me the references. Thanks again!

 yours sincerely,
 Chaofu Wu, Dr.

  ------------------ 原始邮件 ------------------
  发件人: "GMX Xiao"<gmx.xiaos at gmail.com>;
 发送时间: 2010年10月27日(星期三) 晚上6:06
 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...

 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 <xiaowu759 at 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.

 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> 

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