[AMBER] Bonds across the periodic boundaries

From: Xiaoyu Wang <xwang181.hawk.iit.edu>
Date: Thu, 7 Jun 2018 22:32:57 -0500

Dear All,

I want to simulate a long chain polymer. Since it is repeatable for its structure, I want to cut it into a smaller piece and use periodic boundaries to wrap both ends. But I am not sure if I joint the two ends, will AMBER be able to tell that they are just the end of one box and the beginning of another box? Or the program will still bend the chain to joint the both ends.

Or is there other ways to accomplish my thinking?

Best wishes,
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Received on Thu Jun 07 2018 - 21:00:01 PDT
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