Forcekit for simulations preserving topology

[mimakaev]

@golobor @gfudenberg - have you done topological simulations recently? What parameters did you use?

I was thinking that it would be nice to have a forcekit that would be guaranteed to preserve topology. There are a few options.

Recently, Kirill was using polynomialRepulsive (or Grosberg?) force with 10kT cutoff, but also with 0.6 distance between neighboring monomers in harmonicRepulsive. It works, but I thought 0.6 is too short for the bond length.

[golobor]

Hey! I used overlapping particles with extra exceptions too, it seemed to work well for me. Probably, I also had to lower error tolerance and increase the friction a bit - can look it up if that's useful! Anton. (typed on a phone, sorry for brevity and typos)

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On Tue, Dec 22, 2020, 18:53 Maksim Imakaev ***@***.***> wrote: @golobor <https://github.com/golobor> @gfudenberg <https://github.com/gfudenberg> - have you done topological simulations recently? What parameters did you use? I was thinking that it would be nice to have a forcekit that would be guaranteed to preserve topology. There are a few options. Recently, Kirill was using polynomialRepulsive (or Grosberg?) force with 10kT cutoff, but also with 0.6 distance between neighboring monomers in harmonicRepulsive. It works, but I thought 0.6 is too short for the bond length. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#37>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG64CTYGLQWBXL55BDCT33SWDMJPANCNFSM4VF6ISMQ> .

[mimakaev]

@henrik-dahl-pinholt was going to do some topology simulations recently. Maybe a result should be a "topology_preserving_chain" forcekit?

[henrik-dahl-pinholt]

Would be interesting. I am certainly playing around with it now. Currently, I am trying to implement it as a forcekit using the grosberg bond, angle, and non-bonded interaction. Another issue is multi-ring starting configurations which I am currently playing around with as well. Will update you on the progress when there are some results.