[gmx-users] Water molecule error

[Souparno Adhikary]

Hi,

I was encountering an error as the following when running the production
simulation of a protein-membrane system.

*> the cut-off length is longer than half the shortest box vector or longer
*>* than the smallest box diagonal element. Increase the box size or
*>* decrease rlist.*

I increased the shortest box length to the 2.5 times of the shortest box
vector. After that, I am encountering another error regarding the water
molecule.

step 0: Water molecule starting at atom 14720 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
^Mstep 0
WARNING: Listed nonbonded interaction between particles 6528 and 6537
at distance 2.910 which is larger than the table limit 2.232 nm.

Can you please suggest what can I do to fix this?

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.