Re: [AMBER] Protein moving out of the water box

From: David A Case <>
Date: Sat, 21 May 2016 08:21:18 -0400

On Fri, May 20, 2016, Arati Paudyal wrote:
> My protein complex looked ok and they stayed intact for the entire
> simulation. The protein-protein interaction part always remained inside the
> water boundary . The part that is moving in-out of the boundary is a small
> C-terminal tail that is just dangling. I compared my data from 60 ns and 80
> ns (with iwrap) and they are very close. SO I don't think that mattered a
> lot.

Are you sure this is a problem? Remember that no part of the protein is
going outside the solvent: the C-terminal tail is just sticking into the
adjacent unit cell. You might want to use VMD to visualize neighboring cells,
to see if you are getting any protein-protein interactions between images that
you don't want. One explanation for what you describe is that your solvent
box is rather small, so that it is hard to a single unit cell in which all
of the protein appears to "fit" inside the solvent.


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Received on Sat May 21 2016 - 05:30:03 PDT
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