Q - our Molecular dynamics program

Q is a molecular dynamics package designed for free energy calculations in biomolecular systems.

The Q-package has been upgraded and version 5 of the Q-package is now avaliable. New features include:

• support for parallel execution
• periodic boundary condition with constant pressure

The Q5-package is available for registered users on the download page, and for new users after establishing a license agreement.

Contents

1	Introduction
2	Download the program	for licenced users only.
3	Documentation
4	Evaluation version
5	Examples
6	Force field files	for licenced users only!
7	Obtaining a license
8	Support
9	Qusers E-mail list
10	Users' comments	What do users say about Q?
11	Upgrade Qdyn3	Version Qdyn3.77 Nov.9 2000

 

Introduction

Molecular dynamics (MD) simulation can be used to sample the thermally accessible region 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 and (III) linear interaction energy (LIE) calculations of receptor-ligand binding affinities.

The main features which distinguish Q from other MD packages are:

• The spherical boundary. Q is intended for free energy calculations in biomolecular systems solvated in a spherical droplet of explicit water molecules. Using a spherical boundary makes it possible to limit the size of the simulated system, i. e. to focus the simulation on a smaller region such as a binding site, and also makes accurate treatment of long-range electrostatics rather inexpensive.
• The flexibility in choice of force field. The force fields are defined in parameter files, separate from the program and the choice of force field is thus simply a matter of which parameter file to use. These force fields are available:
  • GROMOS87
  • GROMOS96
  • Amber/OPLS
  • AMBER95
  • CHARMM v.22
• The ease of use and learning. The simulation control input and force field definition files are organised in a flexible way and easy to understand and modify. The programs give extensive diagnostics when problems are encountered.
• It runs on any computer and simulates any number of particles. By using dynamic memory allocation Q can simulate biomolecules of moderate size on a personal computer, or very large molecular systems on a super-computer, without any modifications of the program. In addition to the full source code, we offer executable images for

• Windows XP (x86)
• Linux (x86)

Evaluation version

If you want to try Q before requesting a licence, 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 optimisations disabled and therefore run at less than 20% of the speed of the optimised programs. Only Gromos87 force field files are included in the kit.

• Download evaluation kit for windows
• Download evaluation kit for linux

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

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.

• Q version 5 manual in PDF format
• Q version 4 manual in PDF format
• Q version 3 manual in PDF format

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

• Qdyn version history
• Qprep version history
• Qcalc version history
• Qfep version history

Obtaining the program

Licences to use Q are 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 organisations. Licenses are granted to research groups, departments, institutes etc. through a contact person by a signed a licence agreement. There is no need to get a new licence for each additional user or computer within the same organisation. To request a free, non-commercial user licence, follow the steps below:

1. Download and print the licence agreement for non-commercial use (PDF format)
2. Fill in and sign the agreement form.
3. Send the completed agreement to the adress at the top of the form.
   • We appreciate if you include a short letter introducing yourself, your organisation and what you intend to use the software for.
   • If you want to recieve back a copy signed by both parts then include a signed copy.
4. 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, fax the agreement to the attention of Johan Åqvist at the Dept. of Cell & Molecular Biology, fax +46 18 536971 and send e-mail to Johan Åqvist to notify him of the fax message. You must still send the agreement by post.

For commercial use

We are working on a licencing scheme for commercial users, involving a licence 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 licences, send these directly to Johan Åqvist. Bug reports and other queations should be sent to Martin Nervall

Qusers E-mail list

Please note that e-mail list no longer is in use. In the future we aim to construct a Q-forum on this page where you can communicate with other Q-users.