[gmx-users] removing a water molecule

[Ragothaman Yennamalli]

Thanks.
I do get LINCS warning all the time. I had removed two
water molecule, that seemed too close to where the
LINCS warning came for. And started the simulation
again from the scratch and it stopped as mentioned in
my previous message.
Ragothaman
--- Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> Ragothaman Yennamalli wrote:
> > Dear all,
> > I am running a MD simulation, which stops after
> 6ns
> > run with an error saying:
> > 
> > t = 6825.932 ps: Water molecule starting at atom
> 19637
> > can not be settled.
> > Check for bad contacts and/or reduce the
> > timestep.Wrote pdb files with previous and current
> > coordinates
> > 
> > How does one proceed from here? Is removing the
> single
> > water molecule a solution? In that case wouldn't
> there
> > be a conflict between the number of atoms of
> previous
> > trr file and the new one being made?
> 
> Yes, you can't continue from where you are. You
> should have a close look 
> at what's been happening and see if there are any
> other problems. 
> Probably you need a more gentle
> minimization-equilibration regime at the 
> start.
> 
> Mark
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