[gmx-users] protein_ligand error NVT

[Justin Lemkul]

On 11/19/19 10:30 PM, Iman Katouzian wrote:
> Good day.
>
> I have encountered a problem in my protein-ligand simulation as after the
> energy minimization step, when I run the gmx mdrun -deffnm nvt
> I encounter the error segmentation faiulire core dumped :
>
> step 1: One or more water molecules can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Back Off! I just backed up step1b.pdb to ./#step1b.pdb.8#
>
> Back Off! I just backed up step1c.pdb to ./#step1c.pdb.8#
> Wrote pdb files with previous and current coordinates
> *Segmentation fault (core dumped)*

http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system

-Justin

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Justin A. Lemkul, Ph.D.
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