Date: Tue, 22 Feb 2000 07:43:57 -0800
From: David Case
Subject: Re: AMBER PBC images

On Tue, Feb 22, 2000, Alexander Issanin wrote:

>
> The problem, I've meet concerns periodic boundary conditions in SANDER
> run. As result of long run SANDER can push some molecules (in my case it
> was one of two DNA strand) into neighboring cell.

This is not a "problem" per se, since you are simulating a periodic
system; the output files contain only one copy of each molecule in the
system; choosing which molecule to include is to a certain extent a matter
of taste, and of what you wish to do with the results.

In you example, there are two straightforward choices:

(1) Use the "iwrap" variable to control which molecules get written to the
trajectory and restart files. The discussion of this variable in the manual
may also help to clarify what is happening.

(2) Use the "ptraj" program to post-process your restart or trajectory
files in order to "image" them more to your liking.

...hope this helps....dac