Has anyone tried to use Pipeline Pilot scripting to perform Monte Carlo optimization?
I am well aware of MC used in atomistic computer simulations, but I am wondering about the
usage of MC in various cheminformatics models and algorithms.
For example, I have a set of molecules organized in some low dimensional space. I would
like to re-organize those molecules and generate a new configuration (a new set of coordinates)
according to some criteria. The criteria might be agreement with an intermolecular distance
matrix. Perhaps Monte Carlo optimization might be a means to generate alternative configurations
that have reasonable agreement with my distance matrix.
The above example is one possible scenario. I am interested to hear of others who are using
MC methodology and Pipeline Pilot to accomplish various tasks. If you have a protocol that
you are able to share that would be helpful.
Thank you.
Regards,
Jim Metz
