Uppsala Universitet

Q - Our Molecular Dynamics Program

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Free energy calculations in biomolecular systems

Introduction

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:

  • (I) Free energy perturbation (FEP) simulations.
  • (II) Empirical valence bond (EVB) calculations of reaction free energies.
  • (III) Linear interaction energy (LIE) calculations of receptor-ligand binding affinities.

Documentation

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

The latest changes are briefly documented in the version history files:

Evaluation Version

If you want to try Q before requesting a license, we provide an evaluation kit. The kit contains executable images for the Q programs for the Win32/Intel x86 platform (i.e. Windows95, Windows98, WindowsNT running on Pentium-like processors). The evaluation programs were built with all compiler optimizations disabled and therefore run at less than 20% of the speed of the optimized programs. Only Gromos87 force field files are included in the kit.

To get started in setting up your own test simulations, you probably want to look at the Q examples available on-line.

Obtaining the program

License to use Q is offered by the company Uppsala Molekylmekaniska HB which is owned by the Q developers.

For non-commercial use

Our policy is to distribute the program, complete with source code, without charge to academic institutions and to other non-profit organizations. Licenses are granted to research groups, departments, institutes etc. through a contact person by a signed a license agreement. There is no need to get a new license for each additional user or computer within the same organization. To request a free, non-commercial user license, follow the steps below:

  • Download and print the license agreement for non-commercial use (license.pdf)
  • Fill in and sign the agreement form.
  • Send the completed agreement to the adress at the top of the form.
  • We appreciate if you include a short letter introducing yourself, your organization and what you intend to use the software for. If you want to receive back a copy signed by both parts then include a signed copy. When we have recieved and accepted the agreement we will e-mail you the login information that enables you to download the software from our web server. To get access to the software faster e-mail the agreement to the attention of Johan Åqvist at the Dept. of Cell & Molecular Biology. You must still send the agreement by post to the Department of Cell and Molecular Biology at Uppsala University.

For commercial use

We are working on a licencing scheme for commercial users, involving a license fee. Please send inquiries to Johan Åqvist, introducing yourself and your company. The evaluation version is of course available also to prospective commercial users.

Support

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. If you have questions about Q regarding licenses, send these directly to Johan Åqvist ( ). Bug reports and other questions should be sent to Christopher Lind ( ).

Q-user mailing list

The Q-users mailing list is hosted at google-groups:

qmolecular-dynamics

To be included in the list please send a request to: qmoldyn@googlegroups.com