[gmx-users] coarse grained multi-body cut-off distance error

xiao helitrope at 126.com
Mon Oct 5 10:43:37 CEST 2015

Dear Gromacs user,

The coarse grained simulation was done by using the files prepared by the SMOG server.
However, i got an error as follows: 

Not all bonded interactions have been properly assigned to the domain decomposition cells

A list of missing interactions:
               LJ-14 of   2999 missing      1

Molecule type 'Macromolecule'
the first 10 missing interactions, except for exclusions:
               LJ-14 atoms  370 1095           global   370  1095

Program mdrun, VERSION 4.5.4
Source code file: domdec_top.c, line: 356

Fatal error:
1 of the 16106 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (2 nm) or the two-body cut-off distance (2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck

The rlist value is 1.5 in .mdp file, and i give a value of 2 to -rdd, but i still got the problem. 

Please give me some information on the possible reason of the error.

Best wishes


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