Can we ask one bead per heavy atom? [question]

[UnixJunkie]

Also, is the obtained "CG molecule" still flexible if the input molecule was?

[UnixJunkie]

Or, "can we constrain the obtained CG model to have one bead per input molecule heavy atom"?

[tbereau]

Yes, you can, but you'll have to fiddle with the parameters of the model. See objective function in the JCTC paper for detail. I don't know which values you'll need though, so you'll need to look into it.