[AMBER] Questions on targeted MD with explicit solvent

From: Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. <shaowen.hu-1.nasa.gov>
Date: Tue, 14 Apr 2009 14:51:40 +0100

Dear Amber users,

I am doing some tests on the targeted MD and have some questions with explicit solvent:

1. Does the system need to have a periodic boundary or just a water shell without replicate neighbors?
2. Has the technique been applied to big system such as protein-DNA complex?

Thank you in advance,

Shaowen

Shaowen Hu, Ph.D.
Research Scientist
USRA Division of Space Life Sciences
3600 Bay Area Blvd., Houston, TX 77058, USA
Phone: 281-483-1163



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Received on Wed Apr 15 2009 - 01:15:05 PDT