Allow mdrun to start many simulations from a single TPR
Summary
Allow mdrun to start simulations with new velocities to avoid regenerating TPR files.
Use cases
Many ensemble simulations - in particular for free energy calculation - rely on running hundreds or thousands of short simulations of the same system with different random seeds. Presently this requires users to keep regenerating and storing all those TPR files, which can become a major bottleneck in projects with millions of simulations.
Detailed description
Originally our idea was to describe an ensemble of N simulations just with different velocities in a single TPR, but this gets complicated since it can only run on a system with that number of MPI ranks. Instead, we favor the much simpler approach of adding flags to mdrun (and maybe convert-tpr) to allow users to reassign velocities either by drawing a new random seed, or using a user-provided seed on the command line. This seed will also be written to the log file.