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
Received on Fri Feb 26 2010 - 22:00:04 PST
