Does not allow molecules to be limited to the local box in GOMC and move in NAMD in the GEMC and GCMC ensembles

[bc118]

The current setup does not allow molecules to be limited to the local box in GOMC and move in NAMD in the GEMC and GCMC ensembles.

Limiting a molecule in a local box in the GOMC simulations (beta=2 in pdb file) to do GCMC properly, does not allow it to move in NAMD since the NAMD file pdb reads fixed atoms as any non-zero beta values. This can be bypassed in the NVT or NPT simulations to just pass in an alternate NAMD fixed atoms PDB, because the atom numbers do not change; however, this is not the case for GEMC or GCMC.

I think we almost need to write another PDB file out of GOMC, without printing the 2s in the beta column (printing 0s instead), and add another variable to fix atoms based on this new fix to the user options in py-mcmd.

This is primarily an issue when you need to fix atoms in place (beta=1) and need to limit a molecule in a local box in the GOMC simulations (beta=2 in pdb file). Meaning you need to use the fix beta in the NAMD simulation, but only on the betas that are 1.