Re: [AMBER] Reg. Periodic Boundary Conditions

From: David A Case <>
Date: Wed, 5 Feb 2020 07:52:47 -0500

On Wed, Feb 05, 2020, DHEERAJ CHITARA wrote:
>How periodic boundary conditions works with rectangular box and octahedral
>box in amber.

As before, you question is not clear enough for anyone to provide a
answer. Lots of aspects of molecular simulations depend on the boundary
conditions, so asking how it "works" doesn't really tell us what you
want to know. Are you interested in how forces are calculated, how
dynamics are propagated, how neighbor lists are constructed, ....?

Textbooks on molecular simulations (such as the Allen and Tildesley
classic) describe the basic operations of periodic boundary conditions.
Any deep understanding would require a lot of work, and would require
you to become pretty familiar with the innards of Amber codes.


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Received on Wed Feb 05 2020 - 05:00:02 PST
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