From: nida baig <>
Date: Sat, 23 Jul 2016 07:46:45 +0000 (UTC)

In the context of your reply, attach is the image of the protein in water box. After visualization what would you suggest should I repeat the simulation with large solvent box or if I ignore it , will the results and analysis be affect Dr Nida Baig


    On Friday, July 22, 2016 5:28 PM, David A Case <> wrote:

 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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(image/jpeg attachment: protein.jpeg)

Received on Sat Jul 23 2016 - 01:00:02 PDT
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