Try using low-temperature dynamics - see the amber web Questions
area on equilibration. The problem is probably with the basic
nature of minimization, possibly in combination with the starting
coordinates.
Bill Ross
I wondered if there is an alternate type of water, besides the
rigid TIP3P model, available in LEaP for cap and box solvation.
Energy minimization with Sander does not seem to work for TIP3P water,
even using only the steepest-descent method; the energy fluctuates but
does not drop significantly, and the RMS gradient remains high
(~1000 kcal/A). The only option I see in the Leap manual is WATBOX216
which uses the rigid model.
Received on Mon Sep 25 2000 - 12:00:25 PDT
