Contains the settings to run steered MD with pull code restraints between beads i and i+1 on your input string. In addition, to this you need start coordinates to your steered MD simulation (default ...

With computer simulations of >100,000 atoms, the mechanism for the hydrophobic collapse of an idealized hydrated chain was obtained by tiling space with (0.2 nm) 3 cubes and projecting the atomistic ...

This code has been deposited publicly on github. It was originally used to set up and perform string method with swarms of trajectories simulations of the beta2 adrenergic receptor, a G protein ...

Protein conformational change is of central importance in molecular biology. Here we demonstrate a computational approach to characterize the transition between two metastable conformations in ...