[gmx-users] protein_ligand error NVT

[Bratin Kumar Das]

You can minimise the system in vaccum. If it is not running properly there
might be some problem in topology. If it is running proper ...you have to
delete water molecule from the surface of the protein...and then minimize.

On Tue 19 Nov, 2019, 9:32 PM Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> 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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