Are you looking at the system with Swiss PDB viewer? JK.
Can you share with us the settings used for periodic boundary conditions and coordinate wrapping? One cause might be that coordinates are not wrapping, which would leave holes in the original image, which are filled by water molecules in the periodic images.
On Feb 27, 2010, at 12:40 AM, Mark M Huntress wrote:
> Hi, I have a 10Å TIP3P water solvent shell around a protein, and I did MD on just the waters, freezing the protein, with periodic boundary conditions, with slow heat, so I turned off Langevin. After 500 ps the edges of the solvent cube have developed a couple big empty spaces, and the cube looks like a block of swiss cheese. Offhand, does anyone have a good idea of what I might have messed up?
> Thanks
> Mark
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Received on Sat Feb 27 2010 - 06:30:03 PST
