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Re: [lammps-users] Changing boundary conditions in polymer
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Re: [lammps-users] Changing boundary conditions in polymer


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sun, 3 Dec 2017 17:34:33 -0500

before you can change boundaries from periodic to non-periodic without breaking bonds, you have to make certain, that are are no bonds crossing periodic boundaries. as simple as that. in other words, you first have to "disentangle" your system, so that all atoms are inside the same periodic image. for example, you can try to increase your box in that dimension (without changing atom positions) until there is a sufficient separation between the periodic images.

that said, it is probably simpler to start your simulation with s p p boundaries from the very beginning, or when you are using p p p, then you need to insert some kind of barrier that prevents crossings. what is the reason to do a fully periodic simulation first?

axel.

p.s.: giacomo, this *is* a different question.

On Sun, Dec 3, 2017 at 5:15 PM, Giacomo Fiorin <giacomo.fiorin@...24...> wrote:
If you don't like the first answer, please don't ask the same question again.


On Sun, Dec 3, 2017 at 1:12 AM, Rajesh <creativeidleminds@...24...> wrote:
Dear lammps users
I am simulating polyethylene with initial p p p conditions and want to change the conditions to s p p. But when I do this, polymer chains at boundary have broken bonds due to change in boundary conditions. Is there any way in lammps so that whole polymer chain can be confined in in simulation box so that no bonds are broken at boundary?

thanks 
Rajesh

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--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.