Dear Dr. Barnett
Please see the attached the data file and input file. In this data file, there is only one single chain, and the molecule ids of each bead are the same. And I also attached a output file and screenshot of one snapshot of the trajectory. As you can see in the output file `test.out`, the radius of gyration of the system diverges which is due to the breaking of the chain and small parts drift away. You can clearly see this in the snapshot. If I label the polymer chain using the molecule id like 1,2,3,…,50,49,48,….,3,2,1. The result would be same, the chain still break into parts.
Best
Guang
datafile.dat (16.7 KB)
input.in (1.02 KB)
test.out (6.82 KB)
Dear Dr. Barnett
Please see the attached the data file and input file. In this data file,
there is only one single chain, and the molecule ids of each bead are the
same. And I also attached a output file and screenshot of one snapshot of
the trajectory. As you can see in the output file `test.out`, the radius of
gyration of the system diverges which is due to the breaking of the chain
and small parts drift away. You can clearly see this in the snapshot. If I
label the polymer chain using the molecule id like
1,2,3,…,50,49,48,….,3,2,1. The result would be same, the chain still break
into parts.
Best
Guang
So you have no solvent or other chains? Bond swapping is really only useful
for getting a chain equilibrated when it obeys chain statistics - which it
won't in a vacuum.
What is the goal with simulating a single chain in a vacuum?
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.
Best
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.