Implicit water with explicit ions

From: Adrian (
Date: Thu Jul 18 2013 - 13:10:49 CDT


I'm interested in running some simulations using implicit water (as in
the namd tutorial 1-4, for example), but I notice you are not supposed
to explicitly ionize your system in such cases, but I do need to
consider explicitly the ions, as that's my main interest.

If I add the ions to the the pdb and delete water molecules, would it be
correct to continue the procedure for GBIS (generalized born implicit

If not, what would be the correct approach?

Thanks for your time!!

Adrian Palacios

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