AMBER: hybrid remd imaging

From: Geoff Wood <>
Date: Mon, 24 Mar 2008 16:51:51 +0100

Dear Amber Community,

I am curious about the imaging done in hybrid remd calculations.

If I use ptraj commands (see below) to post process a trajectory then
the imaged trajectory looks like what one would expect (see attached
However, if I look at the stripped restart file then the imaging seems
to be a bit strange (see the other attached picture). Could anyone
comment on this?

ptraj commands:

trajin coords
center * mass origin
image origin center
solvent byname WAT TIP3
closest 350 :mask first
trajout coords.strip nobox


Dr Geoffrey Wood
Ecole Polytechnique Fédérale de Lausanne
BCH 4108
CH - 1015 Lausanne

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Apr 18 2008 - 21:13:39 PDT
Custom Search