Re: [AMBER] Best way to implement PBC

From: <>
Date: Wed, 7 Mar 2012 16:22:35 -0500 (EST)


> 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
> advice.

If you can save your setup as a pdb or mol2 file, you can load it into
leap and apply the setbox or set box commands and then save as amber
prm&rst. Note that you will probably have to go through leap anyway and
that means that you need amber-compatible parameter files for your lipid


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Mar 07 2012 - 13:30:03 PST
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