Dear Gromacs users
I am facing this error during free energy calculation of protein-ligand for
which I have applied restrained to some atoms of protein residue and
ligand.
A list of missing interactions:
Restraint Pot. of 1 missing 1
Molecule type 'Protein'
the first 10 missing interactions, except for exclusions:
Restraint Pot. atoms 3437 7908 global 3437 7908
-------------------------------------------------------
Program: gmx mdrun, version 2018.1
Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
MPI rank: 0 (out of 2)
Fatal error:
1 of the 64584 bonded interactions could not be calculated because some
atoms
involved moved further apart than the multi-body cut-off distance (4.47682
nm)
or the two-body cut-off distance (4.47682 nm), see option -rdd, for pairs
and
tabulated bonds also see option -ddcheck
Could anybody please suggest how should I fix this error? I would be really
thankful.
Regards
Sadaf
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