[gmx-users] Water molecule error

[Dallas Warren]

Check the detail at following URL

http://www.gromacs.org/Documentation/Errors

On 7 Nov. 2017 8:12 pm, "Souparno Adhikary" <souparnoa91 at gmail.com> wrote:

> 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.
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