added conditional to platform creation in the OpenMMRunner
added conditional to platform creation in the OpenMMRunner

We want to allow for setting the platform without setting the GPU
indices, say if you want to enforce using CPU, or just use 'CUDA'
without setting the device indices.

Also got rid of the velocities being set separately

ADicksonLab/wepy,ADicksonLab/wepy,ADicksonLab/wepy