[gmx-users] Unstable System

Nikhil Agrawal nikhil.08oct at gmail.com
Thu Oct 10 16:21:15 CEST 2013


when I am running NVT equilibration phase i am getting following error

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4#
Wrote pdb files with previous and current coordinates
starting mdrun 'Gromacs Runs On Most of All Computer Systems in water'
250000 steps,    500.0 ps.

WARNING: Listed nonbonded interaction between particles 6483 and 6507
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

if any one have solution for that. please let me know

Thanks in advance.


Nikhil Agrawal
Project Fellow
Institute of Genomic & Integrative Biology (IGIB)
Mathura Road
New Delhi 110020

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