I realized that quest regarding to figure 1. is my error as the brown
colored balls represent phosphorous atoms and not ions. I am sorry because
of such mistake.
Best wishes to all of you.
Zoran
-----Original Message-----
From: zoran matovic
Sent: Tuesday, February 2, 2016 3:10 PM
To: amber_list
Subject: [AMBER] Amber/tutorial/advanced/tutorial16/
Hi Amber people,
I am doing tutorial 16 on lipid simulation. I have perhaps trivial
questions.
Firstly, I attached three comparative figures.
1. Input cards image shows some differences in the number of ions, that
means the first pic differs from the others. That is web image contains much
more ions than others. Is this consequence of the choice of pic from
different molecule or something else?
2. Min_images and heat_images gave something interesting. Firstly, I suppose
that authors did autoimage and then gave us web_min and web_heat images. If
so and when I did autoimage to my *.rst files I obtained system with quite
different water layers ratio. This means that after autoimage one can see
proportional loosing of water from one side and increasing on the other side
of the bilayer. My question concerns if I did something wrong or this
presents just a consequence of periodic boundary imaging?
Might be that my quests are silly or answered in some earlier posts. If so
I apologize.
Zoran Matovic
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Received on Tue Feb 02 2016 - 09:30:04 PST
