[gmx-users] Error with bonded interactions

Pallavi Banerjee pallavisept at students.iiserpune.ac.in
Sat Dec 12 15:54:01 CET 2015

Hello all,

My system is a coarse-grained polymer in vacuum and I provide bonded
potentials in a tabulated format. After a run of about 10-15 ns, the
following error shows up:

2 of the 146 bonded interactions could not be calculated because some atoms
involved moved further apart than the multi-body cut-off distance (1.54773
nm) or the two-body cut-off distance (2 nm), see option -rdd, for pairs and
tabulated bonds also see option -ddcheck

On having looked at  the trajectory, the system looked just fine.
Even on using -noddcheck, the same error shows up after a few steps. How do
you circumvent this?

Many Thanks!

-Pallavi Banerjee

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