AMBER Archive (2006)

Subject: Re: AMBER: periodic boundary condition question...

From: David A. Case (case_at_scripps.edu)
Date: Mon Oct 30 2006 - 10:32:56 CST

On Mon, Oct 30, 2006, HL Eastwood wrote:
>
> Is it possible to set up a periodic boundary simulation without putting
> waters into it? I wish to examine how a helix aligns with it's own
> dipole and I'd preferrably like a water-free box of 8 x 8 x 20
> Angstroms to test it with.

There are two similar but different ways to do this in LEaP:

1. use the setBox command, as already discussed in other e-mails.

2. use the "set" command itself:

     set x box { 8.0 8.0 20.0 }

(where "x" is the name of your gas-phase unit.) This second option looks more
like what you want.

...good luck...dac

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