periodic boundaries in a molecule type

User discussions
1

i faced this problem while doing the simulation by gromacs
Program: gmx mdrun, version 2020
Source file: src/gromacs/pbcutil/mshift.cpp (line 904)

Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 52 atoms. The longest distance involved in such interactions is
9.359 nm which is above half the box length. Either you have excessively large
distances between atoms in bonded interactions or your system is exploding.

2

Hi,

you can use a visualization software to understand what happen to your system . This may allow you to understand where the problem is.

Best regards
Alessandra