AMBER Archive (2002)

Subject: periodic box

From: Craig A Bayse (CBayse_at_odu.edu)
Date: Mon Nov 04 2002 - 10:49:53 CST

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?