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

英雄不再寂寞 xiaowu759 at qq.com
Sun Oct 24 02:04:09 CEST 2010

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
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        Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff, 
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                                 :-)  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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