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-- Peter Schmidtke ---------------------- PhD Student at the Molecular Modeling and Bioinformatics Group Dep. Physical Chemistry Faculty of Pharmacy University of Barcelona On Sat, 27 Feb 2010 09:08:54 -0500, Nicholas Musolino <musolino.MIT.EDU> wrote: > 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 >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Feb 27 2010 - 13:00:03 PST