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Hello, Amber:
I have a question regarding to the periodic water box. I solvated my
protein model with WATBOX216 with the 10A minimum distance. After two
steps of equilibrations, constant pressure 50 ps & constant temp and
pressure 50 ps, the system was fairly stable and then subjected to
production MD runs. I notice that the water molecules were spread at the
edges and the box was no longer rectangular after the equilibrations. The
water box remained non-rectangular during the MD simulation. In my sander
input, I set ntb=2 which refers to constant pressure for periodic
boundary conditions.
My question is about the minimum distance of water box used to solvate
system. Is this minimum distance only used for setting up the initial
system? After system is equilibrated, it will be no longer useful?
Thanks for your input.
Bo
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Received on Thu Apr 14 2005 - 07:53:00 PDT
