Re: How to confirm water box is big enough?

From: Jin Liu (jliunih_at_gmail.com)
Date: Tue Mar 30 2010 - 15:44:26 CDT

Thank you very much David. I can tell from the VMD that there is no direct
interact between protein and its image. But is there a way that I could
measure the shortest distance between protein and its images during the
simulation to make sure? I need to address it to a reviewer's comment. Thank
you very much.

On Tue, Mar 30, 2010 at 4:13 PM, David Tanner <guacamoleo_at_gmail.com> wrote:

> One thing, and there may be several others, you must test is to verify that
> the protein doesn't directly interact with itself. This means that no atom
> in the protein should ever be within CUTOFF of any atoms in any periodic
> image.
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> David E. Tanner
> Theoretical and Computational Biophysics Group
> 3159 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801
> http://www.linkedin.com/in/davidetanner
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> On Mar 30, 2010, at 2:29 PM, Jin Liu wrote:
>
> Hi,
>
> I did a few MD simulations with the the minimum distance from the protein
> to the edge of the water box as 10 angstrom. The simulations ran smoothly
> without any problem. I am wondering what I could do to confirm the water box
> is big enough? Should I measure the distance between the protein and its
> image in the other boxes during the simulation? Or what else can I do to
> convince people that the water box is not too small?
>
> Thank you very much.
>
> Best regards,
>
> Jin
>
>
>
>

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