Re: [AMBER] Best way to implement PBC

From: Ben Ahmady <>
Date: Wed, 7 Mar 2012 15:26:35 +0000

Hi AMBER users & developers,

I'm trying to run a bilayer through AMBER and have developed a 'box'
with defined dimensions for a layer of water, followed by bilayer,
bilayer, then more water (with sodium ions interspersed). I've done all
of that in Packmol - including the water, and sodium ion additions. What
I'm unsure of is the best way to implement periodic boundary conditions
in my minimisation/MD simulations, and would be very grateful for any

Best wishes


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Received on Wed Mar 07 2012 - 07:30:03 PST
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