In case of a segmentation fault, run it under a debugger (like gdb, or lldb) to figure out at which line in the code it crashes. That can help to pinpoint what the problem might be.
About modeling flexibility, different types of flexibility requires different treatments. So it depends on the situation. For flexibility around equilibrium positions simple atom-displacements might suffice. For large scale movements you will need to use MC/MD-hybride moves since it is collective motion on longer time scales.
About modeling flexibility, different types of flexibility requires different treatments. So it depends on the situation. For flexibility around equilibrium positions simple atom-displacements might suffice. For large scale movements you will need to use MC/MD-hybride moves since it is collective motion on longer time scales.