> In my studies
> the water bridges are of vital importance and as the run goes on the
> bridges tend to diminish.
Assuming you have used iwrap=1 or imaged with ptraj, the water
bridges really are being lost. In this case you could view it as
a problem with the force field and 'make it right' by identifying
the waters you want to keep and applying distance restraints to
keep them in place.
Bill
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 14 2010 - 10:00:04 PDT
