Periodic boundary conditionds-Surface Energy

From: Rahul Bhowmik (Rahul.Bhowmik_at_ndsu.edu)
Date: Tue Nov 06 2007 - 12:46:06 CST

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Dear all:

I want to simulate a mineral surface and to calculate its surface
energy. For this, I have to use periodic boundary conditions in such way
that it does not repeat in the constructed surface side. e.g. let say, I
have constructed a (001) surface of a cubic lattice system, then the
periodic boundary conditions should be on negative z direction not on
positive z direction with full PBC on x and y directions. Is it
possible to preform this on NAMD and how? Also, in this case what should
be my PME grid size?
Please let me know any suggestions/answers regarding this.

Thank you

Regards
Rahul Bhowmik
Post Doctoral Fellow
Department of Chemical and Biomolecular Engineering
Johns Hopkins University
Baltimore, MD-21218
Phone: (410) 516-7308 (Office)
      (701) 388-5477 (Mobile)

• Next message: Samuel Coulbourn Flores: "problem with NAMD RNA run"
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• In reply to: Victor Ovchinnikov: "Re: forces on atom"
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