WEB Implementation of plumed in simona simulation package for free energy calculations
Protein/peptide – surface interactions play a highly-important role in bio applications such as medical implants, bio-sensors, biological/electronic interface, etc. Calculations of such complicated systems demand a lot of computational resources. The effective implicit surface model (EISM) for fast and efficient calculation of interaction of proteins/peptides with inorganic surfaces was developed in the group of Professor Dr. Wolfgang Wenzel. All EISM simulations are performed within simulation package SIMONA (SImulation of MOlecular and NAnoscale systems) , which is freely available to academic users (http://int.kit.edu/nanosim/simona). We have recently successfully implemented PLUMED  in SIMONA for performing umbrella sampling simulations for obtaining free energy, employing WHAM (the weighted histogram analysis method) .
 T. Strunk, M. Wolf, M. Brieg, K. Klenin, A. Biewer, F. Tristram, M. Ernst, P. J. Kleine, N. Heilmann, I. Kondov and W. Wenzel, Journal of Computational Chemistry, 2012, 33, 2602-2613.
 M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R.A. Broglia and M. Parrinello. PLUMED: a portable plugin for free energy calculations with molecular dynamics, Comp. Phys. Comm. 2009, 180, 1961.
 A. Grossfield, WHAM: the weighted histogram analysis method, version 2.0, membrane.urmc.rochester.edu/wordpress/