From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Jun 21 2013 - 03:50:35 CDT
Hello:
May I ask which one of the examples provided with the recent "Using
collective variables to drive molecular
dynamics simulations" by Fiorin-Klein-Henin could help with problems of
blind ligand-protein docking? I am comparing with "Sampling protein motion
and solvent effect during ligand binding" by Parrinello and associates
www.pnas.org/cgi/doi/10.1073/pnas.1112181108, which was based on
well-tempered metadynamics. This means that I am considering whether such
problems of interaction between proteins and ligands can be treated with
NAMD without the PLUMED plugin. It would simplify the life of NAMD users.
Thanks
francesco pietra
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