AMBER Archive (2003)

Subject: Re: PBC without solvent

From: caldwell_at_heimdal.compchem.ucsf.edu
Date: Tue Mar 18 2003 - 10:21:40 CST

You can set up a "box" in Leap, after you have your
system ready simply do "setbox <unit>" and leap will
setup a minimal box around your unit. You'll have to
edit prmcrd by hand to change the size of the box
if you aren't statisfied with leap's choice (it's the
last line in the file).

jim

On Tue, 18 Mar 2003, Franck Chevalier wrote:

> Good Afternoon,
> I have a new question about using Periodic boundary condition in AMBER
> 6.0. Is it possible to run PBC dynamics without including solvent in my
> input files (.crd and .top)? I would like first to equilibrate my system
> with PBC before adding the solvent (water). I read that the dimensions
> of the box have to be written in the .crd and .top files.
> Could you please help me again ?
> Thanks a lot,
> Franck
> 

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James W. Caldwell                         (voice) 415-476-8603
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