Hey :)
I'll make a try to be a bit more constructive :p
First of all, always try to think out of the box, especially with PBC :D
The problem may be due to overlapping atoms/molecules, pushing each other
out during energy minimization. When merging boxes, be careful not to
introduce overlaps, by 1.
On 4/3/13 9:46 PM, Abhinav Agrawal wrote:
Hi,
I have a polymer box on which I wish to apply energy minimization.
However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess this is because periodic conditions are not applied.
My em.mdp file is:
> > Hi,
> >
> > I have a polymer box on which I wish to apply energy minimization.
> However,
> > when I do energy minimization runs to polymer chain unravels and goes out
> > of the box. I guess this is because periodic conditions are not applied.
> >
> > My em.mdp file is:
> >
> > >
> > > ;
> > >
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