[gmx-users] A list of missing interactions

[Alessandra Villa]

Hi,
my suggestion is to follow the indication that you got from the error
See the mdrun " option -rdd, for pairs and tabulated bonds also see option
-ddcheck"
Best regards
Alessandra



On Wed, Jan 15, 2020 at 12:33 AM Sadaf Rani <sadafrani6 at gmail.com> wrote:

> 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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