From: David A Case <>
Date: Fri, 22 Jul 2016 08:29:04 -0400

On Fri, Jul 22, 2016, nida baig wrote:

> I have run 50ns simulation of an intrinsically disordered protein. The
> protein's C-terminal region is very flexible and when I visualize the
> mdcrd of the trajectories two to three residues of the protein comes out
> of the water box. I use the under mention commands to re-image the mdcrd
> trajectories but still the protein comes out of the water box. Actually
> it comes out and goes back again than flexes  out again. Is this is
> going to affect my analysis if yes how to correct it.

In periodic systems, residues never "come out of the box": they just move
to the adjacent water box. Imaging tries to pack the waters into a compact
unit cell around the origin. If the entire protein cannot fit into such a
box, it will appear that some residues are outside.

If this is indeed the problem, you can (a) ignore it; (b) use a larger solvent


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Received on Fri Jul 22 2016 - 05:30:03 PDT
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