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.xi...@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@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 <xiaowu...@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.
xiaowu...@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)
xiaowu...@linux-s38y:~/workshop>
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