AMBER Archive (2002)

Subject: Re: periodic box

From: David A. Case (case_at_scripps.edu)
Date: Mon Nov 04 2002 - 12:32:11 CST

On Mon, Nov 04, 2002, Craig A Bayse wrote:

> I having a little trouble with periodic boxes. During an MD simulation,
> the box does not remain uniform, the edges flare out such that it's no
> longer regular. I am using the input and pdb files from the DNA tutorial
> on the website, so I assume these would work properly. I have also tried
> to set boxes using setbox and set. What should I be doing?

You probably just need to "re-image" your system to move all atoms to the
central unit cell. See the "image" command in ptraj, or the iwrap variable
in sander.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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