AMBER Archive (2008)

Subject: AMBER: hybrid remd imaging

From: Geoff Wood (geoffrey.wood_at_epfl.ch)
Date: Mon Mar 24 2008 - 10:51:51 CDT

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
picture).
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

Thanks,

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

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