[AMBER] Non-periodic boundry condition simulation

From: Nagar, Hemant <hn533621.ohio.edu>
Date: Wed, 1 Dec 2021 23:27:43 +0000

I wanted to simulate a system which has periodic boundary conditions in two direction and non-periodic boundary condition in third direction(e.g. simulation box is periodic in X,Y but non periodic in Z).I am new to AMBER. I did found a tutorial regarding such system on amber mailing list but the link is not working. The excerpt of that mail is following-

"Anyway, if you really need to run a non-periodic simulation without some
kind of restraint you will always see water molecules boiling off into
vacuum, as you would see in reality if you heated a droplet of water to 300K
in a vacuum. In Amber you can use a solvent cap to solvate your system, this
will add a restraint force around molecules at the edge of the cap that acts
to keep them inside the water sphere. The amber 8 QMMM tutorial
) shows you how to create such a system. With classical simulations you can
also have an implicit solvent field around the outside of the solvent cap.
Note, however, that such a solvent cap method is likely to give you very
artificial pressures within the solvent cap unless you set it up very
carefully. The only reason it is recommended in the Amber 8 QMMM tutorial is
because periodic boundaries are not supported here. The Amber 9 update to
this tutorial will use regular PME periodic boundary conditions."

How I can simulate such system in AMBER?

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Received on Wed Dec 01 2021 - 15:30:02 PST
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