AMBER Archive (2009)

Subject: [AMBER] Questions on targeted MD with explicit solvent

From: Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (
Date: Tue Apr 14 2009 - 08:51:40 CDT

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 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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