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
Fugui
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