Re: [AMBER] Bonds across the periodic boundaries

From: Thomas C Bishop <>
Date: Fri, 8 Jun 2018 11:53:09 -0500

I reported a simulation in 2005 in which I did exactly this w/ ~146bp of
dsDNA and it seemed to work at least on the 10 ns time scale .

The structure was built w/ amber/leap but trajectory computed w/ namd

There are some issues to be aware of. such as scaling the box
"stretches" the molecule and the molecule is topologically circular so
extra constraints are imposed and likely many many more that could be

Journal of Biomolecular Structure &
Dynamics, ISSN 0739-1102
Volume 22, Issue Number 6, (2005)
©Adenine Press (2005)

          Thomas C. Bishop
Hazel Stewart Garner Associate Professor
         Chemistry & Physics
          Tel: 318-257-5209
          Fax: 318-257-3823
On 06/07/2018 10:53 PM, David Cerutti wrote:
> 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.
> Dave
> 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 Fri Jun 08 2018 - 10:00:03 PDT
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