Hello,
This is mainly due to periodic imaging conditions. By default (if
'anchor' option is not specified) "autoimage" will center the system
according to the first molecule.
One could use "center :first_lipid_residue-last_lipid_residue" (by
replacing accordingly with residue numbers) in order to have the
bilayer centered in the box. This command can be followed by "image"
to wrapped back the water molecules inside the box.
Hope this can help.
Jean-Marc
Quoting zoran matovic <zmatovic.kg.ac.rs>:
> 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 - 07:00:03 PST
