yeah, whta a silly question. What I should ask is to find the minima where the increasing gradient is not that big and sharp. But got very small gradient.

If I find the minimized the solution, and run the simulation.step(), that potential energy increases rapidly over the steps. I 'd like to find the potential energy minima, where the potential energy doesn't increase over the step.

Thanks, I am going to write script to find global minima of potential energy for any protein.
I find that minimize function just found local minima. Is there any module or function that i can use for the global minima with openmm?

1. May I ask which program language performs best please? c++? 2. And what is the maxIteration argument in minimizeEnergy function? 3. what is the difference between maxIteration(in minimizeEnergy function) and nsteps (in simulation.step()) 4. And which function actuall starts simulation? minimizeEn...

I'd like to get minimized energy from pdb file. I want to get this as soon as possible, and the result should be the minimized one. My questions are 1. Can i get this by just increasing steps? 2. Which machine works best for pdb file simulation? 3. Is multi-gpu helpful? 4. Is multi-node linked gpus ...