[AMBER] membrane protein simulation

From: Victor Ma <victordsmagift.gmail.com>
Date: Tue, 26 May 2015 14:13:48 -0700

hello Amber community,

I am following the Amber Tutorial 16 on running lipid simulation and I am
in the equilibration stage with no restrains at all. Here is my input file:

I am checking the output trajectory in VMD and I am not quite sure whether
the lipids look all right. They are kind of loose especially the ones on
the edge. When I visualize them dynamically, it feels like a few of them on
the boundary are "appearing" and "disappearing". I suppose that's the
periodic boundary box? The trajectory has been re-imaged using all the
protein residues as centre. Also I calculated the "lipids per area" and
clearly they are not converged yet. But I am a bit surprised. Because in
the tutorial, lipids seem to have converged rather fast at the beginning of
the simulation.

I attached some pictures and look forward to any comments!

Thank you!!


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Received on Tue May 26 2015 - 14:30:03 PDT
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