AMBER Archive (2007)

Subject: AMBER: question about iwrap

From: Kailee (kaileeamber_at_googlemail.com)
Date: Wed Jul 11 2007 - 08:17:29 CDT

Dear all,

As said in AMBER manual, set iwrap=1 can wrap the trajectory files into the
primary box that can make structure more visually but can mess up diffusion
and other calculations. I am looking at the gas molecule diffusing into a
protein, and need to look at the gas diffusion pathways, what I want to ask
is when I look at the diffusion pathways should I reimage the trajectories
into the primary box or not? as after wrapped into the primary box, the gas
trajectories are quite different from those before wrapping and become
incontinuous. I am now a bit confused, which (before or after wrap) states
are the real situation that I need to do my analysis? Thank you very much
for your help.

Best regards,
Kailee

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