Sander_classic to Sander switch

From: Michael Cooney <>
Date: Thu 26 Oct 2000 16:10:59 -0400 (EDT)

Dear Amber users,

On a protein:DNA complex solvated by a water box I have had
to use the old sander_classic to do simulated annealing on the
solvent water while freezing the solute since apparently belly
dynamics is not compatible with PME (is this correct?) My question is,
after simulated annealing to equilibrate the water, is it feasible
to switch to the new sander with PME on, and allowing the whole
system to move? For the simulated annealing I used nmropt to ramp
the temperature from 5K to 300K, hold at 300K, then cool back down to 5K,
so I would be starting at 5K again and ramping up to 300K, followed
by a production run.

Thanks very much for your help.


Michael Cooney
Department of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602
Received on Thu Oct 26 2000 - 13:10:59 PDT
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