MOLpull: A tool for molecular free energy reconstruction along a pulling coordinate

By Lisa Felberg1, Ignacio Franco1, Martin McCullagh1, Mark Ratner1, George C. Schatz1, Marcelo Carignano1

1. Northwestern University

Estimates the force required for stretching a molecule and determines the potential of mean force along the extension coordinate.

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Version 1.04 - published on 22 Aug 2014

doi:10.4231/D33J39229 cite this

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This tool performs a Weighted Histogram Analysis (WHAM) using molecular dynamics (MD) for statistical sampling along an unfolding pathway. TINKER 4.2 [1] and the MM3 force field [2] are used for the MD propagation. The tool is useful in computing the PMF of arbitrary molecules. A schematic representation of the computations and the system that they model can be described as follows: a molecule is attached to a surface and an AFM tip. The distance between the surface and the cantilever (L) is controlled while the force exerted, F, fluctuates. The instantaneous applied force is measured by determining the deflection of the cantilever from its equilibrium position and is given by: F(t) = -k(ξ(t) - L) where k is the cantilever force constant and ξ(t) is the fluctuating molecular end-to-end distance.


[1] J. Ponder, TINKER: Software Tools for Molecular Design 4.2 (Washington University School of Medicine, Saint Louis, MO, 2004). [2] N. L. Allinger, Y. H. Yuh, and J. H Lii, J. Am. Chem. Soc. 111, 8551 (1989). [3] S. Kumar, D. Bouzidam R. H. Swendsen, P. A. Kollman and J.M. Rosenberg J. Comput. Chem. 13, 1011 (1992) [4] I. Franco, G.C. Schatz and M.A. Ratner J. Chem. Phys. 131, 124902 (2009)

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Researchers should cite this work as follows:

  • Lisa Felberg, Ignacio Franco, Martin McCullagh, Mark Ratner, George C. Schatz, Marcelo Carignano (2014), "MOLpull: A tool for molecular free energy reconstruction along a pulling coordinate," (DOI: 10.21981/D33J39229).

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