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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: Giacomo Fiorin <giacomo.fiorin@...24...>
Date: Mon, 4 Dec 2017 09:26:48 -0500

It may be possible, depending on the length of the chains, to simulate the system above the melting temperature in the NVT ensemble, and then use fix deform to gradually increase one unit cell dimension.  This should create eventually an air gap.  It's up to you then whether to continue running with p p p, or switch to s p p.

But if the polymer chains as so long as to have multiple entanglements each, you should probably look into rebuilding the initial configuration without PBCs in one direction.

Giacomo

On Sun, Dec 3, 2017 at 9:55 PM, Rajesh <creativeidleminds@...24...> wrote:
Dear Axel
Thank you for your quick response. Actually initial structure was prepared using some other software and that software does not go give other option than p p p. So, no choice than to start with p p p. Can owrap command in pizza.py accomplish this or any command in vmd?

On Dec 4, 2017 04:24, "Giacomo Fiorin" <giacomo.fiorin@...24...> wrote:


On Sun, Dec 3, 2017 at 5:34 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
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.

You're right, I misunderstood "ps p p" as a typo for "s p p".
 

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

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