search

open2c / polychrom

Chromosome polymer simulations and in silico capture experiments
MIT License
46 stars 16 forks source link

Forcekit for simulations preserving topology #37

Open mimakaev opened 3 years ago

mimakaev commented 3 years ago

@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 commented 3 years ago

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)

On Tue, Dec 22, 2020, 18:53 Maksim Imakaev notifications@github.com 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 https://github.com/open2c/polychrom/issues/37, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAG64CTYGLQWBXL55BDCT33SWDMJPANCNFSM4VF6ISMQ .

mimakaev commented 2 years ago

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

henrik-dahl-pinholt commented 2 years ago

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.