Dihedral angle move set

Hi Mamta,

If the other dihedrals and angles are held constant for the entire simulation, then there may be a couple ways of accomplishing what you want.

For example, a UA model of pentane has two dihedrals, 1-2-3-4 and 2-3-4-5. Ordinarily, pentane would be parsed into 3 fragments for a Cassandra simulation: 1-2-3, 2-3-4 and 3-4-5. Each regrowth move will sample fragment conformations with new angles, and then assemble those fragments with new dihedrals.

However, if you only want to sample the first dihedral 1-2-3-4, then you could prepare a simulation using two rigid pentane fragments: 1-2-3, 2-3-4-5. In this case, each regrowth move will assemble the two fragments with a different dihedral 1-2-3-4.

Does that sound like what you want?

Cheers,
Ryan

Great. Let us know if you need help creating the necessary fragment files as the Python scripts we've bundled with Cassandra likely won't work for this.