Re: My protein went out of the water box in SMD. Would it have a bad effect on the result?

From: Roman Petrenko (
Date: Mon Jun 29 2009 - 12:57:38 CDT

Please, keep in mind that if you are using periodical boundary
conditions (PBC), the protein is _always_ submerged in water due to
periodicity of the system. Load your trajectory in VMD, and then you
can see other images of your system by
Graphics->Representations->Periodic and then check +Z and -Z.

On Fri, Jun 26, 2009 at 4:02 AM, wayj86 wayj86<> wrote:
> Dear all,
> I found it is difficult to make sure the protein keep in the water box
> during the whole SMD process unless with a very big box. Now my protein went
> out of the box with more than 10 residues and 14 angstrom off the water
> boundary in the -Z direction. The distance between the "went-out" part and
> the protein in the next cell was 13 angstrom. I have red the NAMD tutorial
> but still want to ask you some questions:
> (1) Althought the protein should be merged in the water box when imposing
> periodic boundary conditions, was the "went_out" phenomenon completely
> unacceptable?
> (2) In my situation, would it have a bad effect on my result? Do I have to
> redo the SMD again?
> (3) Is there any literature about this phenomenon which explain it in
> detailed?
> Thank you in advance.
> --
> The future is now!

Roman Petrenko
Physics Department
University of Cincinnati

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