Just to add to what Dave said, do not just change ntb. Other things need
changing too, like your cutoff. I suggest looking at a sample input meant
for periodic simulations.
On May 14, 2016 5:53 PM, "David A Case" <david.case.rutgers.edu> wrote:
> On Sat, May 14, 2016, Iqbal, Muhammad Sajid wrote:
> >
> > I performed MD simulations on a box of dimension 300 x 300 x 300. I
> defined
> > the dimensions using the following command.
> >
> > setbox mybox vdw
>
> This sets up a periodic simulation, although doing it this way is rather
> rare,
> and it's not clear why it gives you 300x300x300.
> >
> > imin = 0, ntb = 0,
>
> Setting ntb=0 then causes Amber to ignore the periodic box. This might
> not be
> a very well-tested code path. Ordinarily, you should set ntb=1 if you
> want a
> periodic simulation, and ntb=0 for a non-periodic one; and these settings
> should match what you did when you set up the system in LEaP in the first
> place.
>
> ....dac
>
>
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Received on Sat May 14 2016 - 15:00:05 PDT
