Re: [AMBER] Bonds across the periodic boundaries

From: David Cerutti <>
Date: Thu, 7 Jun 2018 23:53:33 -0400

Amber cannot do this. I have floated ideas about how to accomplish this,
but so far it is not implemented. I wish we could do it with NMR
restraints to improvise, but this is not possible either--everything in the
bonded terms works according to a representation whereby whole molecules
diffuse in space and the local interactions do not see images of the atoms
they need.


On Thu, Jun 7, 2018 at 11:32 PM, Xiaoyu Wang <> wrote:

> 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,
> Andy
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Received on Thu Jun 07 2018 - 21:00:02 PDT
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