AMBER Archive (2003)

Subject: AMBER: MD simulations on small molecules immersed in sparse water shell

From: Junmei Wang (JWang_at_encysive.com)
Date: Tue Sep 16 2003 - 11:42:56 CDT

Dear AMBER users:

I am running non-periodic boundary MD simulations for a set of middle-sized
molecules (50-100 atoms). Each is immersed in a sparse water shell (10 to
20 TIP3P water, generated using solvateshell in LEAP). What is the best way
to keep solvent molecules from drifting away from the solute along the MD
simulations? This is no water cap information in the topology files if
solvent molecules are added using solvateshell instead of solvatecap.

Thanks

Junmei

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