Recommendations from Anton for avoiding exploding polymers
- integrator choice:
- variableLangevin integrator recommended
- takes an error tolerance instead of a timestep variable (e.g. 10^-4)
- thermostat = high values high friction
- mass_scale = argument of init of simulation (see openmmlib.py)
- attractionRadius (be careful about interaction over other polymers).
- wiggle_dist = higher more oscillation, less chain crossing.
- local energy minimization with attractive potentials might lead to super-position.
- Try global energy minimization.
conlen = 1 nm * length_scale (=1).
- smooth square well force
- polynomial force
- sticky particles should be extra hard.
- every particle has a charge (sticky yes no) repulsion strength yes no.
- extra repulsive force
- try hard-core forces (very large potential energy at overlap).
dynamic adjustments (changing parameters during simulation)
- things of interest to change: friction
- crude way, use output as input
- system block
- try energyMinimization in place of localEnergyMinimization
- avoid any collapsed pairs (they just get worse). — this is time to quit