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 - 15:00:03 PDT
