[gmx-users] Water molecule error

Souparno Adhikary souparnoa91 at gmail.com
Tue Nov 7 10:12:22 CET 2017


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

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,
Department of Microbiology,
University of Calcutta.

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