Fix convert-tpr segfault when no velocities are present in the tpr file

Previously, convert-tpr implicitly expected velocities to be present in the tpr file, which leads to segfaults when this is not the case (e.g. tpr file for energy minimization)

Now:

• Correctly handles subsystem selection via index, even when the tpr does not contain velocities
• Gracefully rejects generation of velocities for such tpr (an additional, unreported problem discovered during investigation)

Fixes #5080 (closed)