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Re: [lammps-users] bond swap within a single chain
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Re: [lammps-users] bond swap within a single chain

From: Wes Barnett <w.barnett@...668...>
Date: Wed, 20 Dec 2017 09:59:01 -0500

On Tue, Dec 19, 2017 at 3:05 PM, Stefan Shi <stefanshi1988@...1125.....> wrote:
You are correct. There is no explicit solvent. I am doing the simulation in the context of Chromosome.  Essentially I am simulating the condensing of a single chain in a bad solvent and I don’t use explicit solvent. The reason of using bond swapping is that in a very long single chain globule, the relaxation time is actually very long due to the similar reason in a polymer melt so I want to use bond swapping to facilitate the equilibration of the system. At least this is plan. But the bond swapping here is different from usual polymer melt case, there you don’t need to worry the breaking of the chain since the bonds are only swapped between different chain not the same chain. 

Guang Shi

Interchain bond swapping should still leave you with one intact chain. Have you run this simulation without bond swapping? I suggest something else is causing your issue. 

James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering