Re: [AMBER] solvent MD - poor equilibration

From: Senthil Natesan <sen.natesan.yahoo.com>
Date: Mon, 17 May 2010 13:14:59 -0700 (PDT)

>I wonder if 40ps is enough. I suggest plotting density to see
>how it is converging.

Actually I sent all the analysis graphs(.png) and a picture of protein-ligand complex picture.
I guess they are all removed by mail-list administrators. Density is pretty stable around 0.94
and it is truncated octahedron (around 6800 TIP3P water molecules).



By the way, is your box cubic or truncated octahedron?

Bill

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Received on Mon May 17 2010 - 13:30:04 PDT
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