Average pressure is calculated for steps between energy outputs. Berendsen method uses average rather then instantaneous pressure. Ratio of first two basis vectors can be fixed for flexible cells. Any contiguous fragment can be wrapped to the periodic cell on output, rather than only wrapping water molecules. Coordinates can be wrapped to the true nearest image for hexagonal or similar shaped periodic cells.
Fixed atoms can be turned off during a run. Most pressure and temperature control parameters can now be changed as well.
Fixed problems reading parm files containing more than 33,333 atoms. Also added changes to read new format parm files from AMBER 7.