implemented features to simulate IDR

[vuqv]

For some proteins that are not fully disordered, there are some folded domains in structure and we want to maintain these domains according to crystal structures.

We will add one more nonbonded force for the contact determined from the crystal structure, e.g Gaussian form, lj12-6 or even lj12, lj6, or whatever we can think about.

The energy factor should be scanned by first, running some short simulations in all-atom resolution, 2) calculating the RMSF of residues in folded domains, tune the epsilon of this force such that the RMSF matches to all-atom results