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Free Energy Calculations in (Bio)Molecular Systems


Molecular dynamic (MD) simulations can be used to sample the thermally accessible regions of conformational space of a microscopic model of a molecular system. From the ensemble of sampled structures and their associated potential energies (given by the force field or molecular mechanics potential energy function) it is, in principle, possible to calculate free energies. Quantities such as binding free energies, solvation free energies and activation free energies are particularly interesting to calculate because they are the direct result of thermodynamic or kinetic experiments. It is thus possible both to quantitatively verify calculated results against experimental data and to make predictions which can be tested experimentally. Q is a set of tools for such calculations, tailored for some specific kinds of free energy calculations, namely:

  • Free energy perturbation (FEP) simulations.
  • Empirical valence bond (EVB) calculations of reaction free energies.
  • Linear interaction energy (LIE) calculations of receptor-ligand binding affinities.
  • Bisection Quantum Classical Path (BQCP) calculations of quantum corrections and isotope effects of EVB free energy profiles.
  • On–the–fly residue deletion calculations.


The Q manual is available on-line as a PDF file. You need Acrobat Reader from Adobe to view and maybe print out your own copy.


We are working on new examples and tutorials at the moment. Older tutorials that were designed for previous Q versions can be found here, and should be applicable to Q6 with minor modifications.


The source code for Q6 can be obtained from GitHub:

Pre-compiled Q6 binaries for different platforms are available for evaluation pruposes. To obtain copies, click the link for the relevant operating system:


Q6 is a free simulation package that is distributed under the GNU General Public License, Version 2.0 (GPLv2). The full license can be found here.

© Copyright 2017 Johan Åqvist, John Marelius, Shina Caroline Lynn Kamerlin and Paul Bauer.
The Department of Cell and Molecular Biology Uppsala University, Uppsala, Sweden


If used in published work, please cite the relevant publications:

Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations
P. Bauer, A. Barrozo, B. A. Amrein, M. Purg, M. Esguerra, P. B. Wilson, D. T. Major, J. Åqvist, S. C. L. Kamerlin
To be submitted

Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems
J. Marelius, K. Kolmodin, I. Feierberg, J. Åqvist
Journal of Molecular Graphics and Modelling 16, 213-225, 1998


We have no resources to support users of Q but of course we appreciate a dialogue with you as a user. Particularly, we are anxious to hear from you in the (hopefully unlikely?) case that you discover a bug in the program. If time permits, we may also be able to answer other questions, e. g. about using the program, simulation procedures, or compilation. Bug reports, issues and other questions should ideally be raised on Github (link). Alternatively send an email to the Q-user mailing list (see below) or to Paul Bauer at paul.bauer.q@gmail.com.

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