Strained protein simulation

Hi everybody,

I’m trying to do the same simulation done by M.J Buehler about fracture on a collagen fiber. The only difference is that I apply a constant velocity (not SMD) on a side of the 3 chains and then measure the force on the other one.

I did a first simulation in vacuum and curves seem to fit fairly well with Buehler’s.
Now, with a more powerful computer, I’ve added a rectangular water box (periodic boundary conditions) and the results have changed a lot. The force measured during the entropic elasticity (almost constant force stage) increased almost two orders of magnitud, and also fluctuations are risen up a lot.
Does anyone know that’s a normal behaviour? should I do try with SMD? Any advice?


nope - you could send Buehler an email ...