[gmx-users] Tabulation table error

Ben Tam btam125 at hotmail.co.uk
Tue Sep 6 19:03:45 CEST 2016

Dear gromacs user,

I am trying to learn how to use tabulation table because I need a mix of Lennard Jones and Buckingham interaction. The tabulated simulation ran for a few ps before crashing with this error:

A list of missing interactions:
               Angle of    730 missing      1

Molecule type 'MOL'
the first 10 missing interactions, except for exclusions:
               Angle atoms  226  524  516      global   226   524   516

Back Off! I just backed up dd_dump_err_0_n2.pdb to ./#dd_dump_err_0_n2.pdb.3#

Back Off! I just backed up dd_dump_err_0_n1.pdb to ./#dd_dump_err_0_n1.pdb.3#

Back Off! I just backed up dd_dump_err_0_n3.pdb to ./#dd_dump_err_0_n3.pdb.3#

Back Off! I just backed up dd_dump_err_0_n0.pdb to ./#dd_dump_err_0_n0.pdb.3#

Program gmx mdrun, VERSION 5.1.1
Source code file: /dev/shm/tmp.PwtfSrm0uJ/gromacs-5.1.1/src/gromacs/domdec/domdec_topology.cpp, line: 435

Fatal error:
1 of the 3954 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.45 nm) or the two-body cut-off distance (0.9 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

I don't really understand what is going on here. Is it because my tabulation table is wrong? I have been following the instruction from the following link:


Thank you very much for your help!

Tabulated Potentials - Gromacs<http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials>
Constructing the Table(s) The GROMACS manual, section 6.7, describes the requirements for the construction of the tabulated potentials. The format of the lines in the ...

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