Re: How to confirm water box is big enough?

From: David Tanner (guacamoleo_at_gmail.com)
Date: Tue Mar 30 2010 - 15:13:10 CDT

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
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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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