Re: [AMBER] Question about lipid simulation

From: Ross Walker <>
Date: Wed, 13 May 2015 10:59:52 -0700

Hi Victor,

You need to reimage your simulation so that all the molecules are visualized as being in the central box. This is a normal occurrence that is covered in the introductory tutorials - I would suggest taking a look at them as well as the documentation for autoimage action in cpptraj.

All the best

> On May 13, 2015, at 10:51 AM, Victor Ma <> wrote:
> hello all,
> I am following tutorial 16 on lipid simulation. To confess, I did not
> follow the exact same procedure. For the "hold" step, I only ran it once
> instead of the 10 times in the tutorial. My argument is that I am doing
> cpu-based simulation.
> Now I am checking the results and I see that in my system, the water
> molecules are naturally "spreading out" like in a soluble protein system.
> Please see the picture in attachment. However the picture in tutorial
> (after 5ns of production run) looks different. In that picture, all the
> water molecules seem to be still stacking on top and bottom of the lipids
> just like when I first set up the system without running it. I am a little
> confused here. Can someone please clarify this for me? Thank you.
> To provide more information, I also attached the plot of area per lipid.
> Thank you !!!
> Victor
> <lipids.jpeg><printme.png>_______________________________________________
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Received on Wed May 13 2015 - 11:30:02 PDT
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