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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) [1], which is freely available to academic users ( We have recently successfully implemented PLUMED [2] in SIMONA for performing umbrella sampling simulations for obtaining free energy, employing WHAM (the weighted histogram analysis method) [3].

[1] 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.

[2] 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.

[3] A. Grossfield, WHAM: the weighted histogram analysis method, version 2.0,

Dr. Mikhail Suyetin
Karlsruhe Institute of Technology (KIT)
Additional Authors:
  • Dr. Saientan Bag
    Karlsruhe Institute of Technology
  • Prof. Dr. Wolfgang Wenzel
    Karlsruhe Institute of Technology