softmaterialslab/np-assembly-lab

Simulates assembly of nanoparticles and oppositely-charged linkers under different physiological conditions. Outputs are structural information such as pair distribution functions.

np-assembly-lab's Issues

Add examples

It would be nice to have examples parameters and outputs.

Simulation fails in Cluster mode

I tried running the simulation in 'Cluster Mode' with default parameters and the simulation run failed.

Simulation running without update in progress bar

While trying to run the simulation after tuning the default parameters, the simulation is running forever with no update in the progress bar. Below are the parameters I used,
NP charge (Q in e): -1000
Linker density (in units of NP density): 50
Salt concentration (M): 0.1

Simulation run time exceeding an hour

The Nano Particle Assembly tool simulation ran for more than an hour without any update in the progress bar, and eventually I had to cancel the simulation. This issue seems to occur approximately one in twenty times I try to run a simulation.

Atoms appears outside the cube

While the simulation is running the atoms (red) appears to be outside the cube at some instances in the simulation snapshot page.