Connecting the user-friendly molecular graphics program VMD to the widely adopted MD program NAMD, QwikMD allows its users to setup a molecular simulation in just a few minutes, allowing for quickly study of point mutations, partial deletions or even steering experiments. While making it easy for a new user to perform simulations, QwikMD also works as a learning tool with several "info buttons" where the theoretical background underlying the procedures is provided.

Recent News and Announcements

QwikMD at Hands-On Workshop on Computational Biophysics at Pittsburgh

QwikMD will be presented during the next Hands-On Workshop on Computational Biophysics, at Pittsburgh Supercomputing Center, Pittsburgh, PA, May 21 - 25, 2018.

VMD 1.9.4 alpha

QwikMD updates in VMD 1.9.4 (alpha). QwikMD had several updates on the latest VMD alpha version and has now the first implementation of the QM/MM interface. In order to run the simulations in the "Live Mode" and/or run QM/MM simulations, the user needs to install the nightly build of NAMD.

VMD 1.9.3 Release

QwikMD is now available on VMD 1.9.3. Employing QwikMD, a user is able to setup MD simulations in just a couple of minutes, allowing quick studies of point mutations, partial deletions and even atomic force microscopy experiments. It is also possible to use QwikMD to prepare Molecular Dynamics Flexible Fitting simulations, which integrates Molecular Dynamics simulations with density maps from cryo-EM experiments.

Availability

QwikMD is available free of charge on VMD 1.9.3 and newer.

Download VMD for free here

To perform Molecular Dynamics simulations you will also need the widely employed NAMD program, which is available free of charge here.

QwikMD beta . The latest version of the QwikMD including the most recent bug fixes can be downloaded here (last update on April 20, 2018). Please follow the instructions in the README file included in the qwikmd folder on how to install the beta version.

Employing QwikMD on your research? Please don't forget to cite us: J.V. Ribeiro, R.C. Bernardi, T. Rudack, J.E. Stone, J.C. Phillips, P.L. Freddolino, K. Schulten; QwikMD: Integrative Molecular Dynamics Toolkit for Novices and Experts; Scientific Reports, 6, 26536 (2016)

What is QwikMD?

Providing dynamics to structural data from experimental sources, molecular dynamics simulations permit the exploration of biological macromolecules in unique detail. The last advances in molecular dynamics simulations are moving the atomic resolution description of biological molecules to the million-to-billion atom regime, while a variety of sampling techniques are allowing for the exploration of millisecond regime. Although the advances of molecular dynamics simulations are taking us to a new level of knowledge of macromolecular complexes, the vast majority of molecular dynamics users are interested in simple "brute-force" molecular dynamics simulations of relatively simple proteins. In special, structural biology experimentalists are becoming more interested in performing molecular dynamics simulations to improve their understanding of protein structure/function relationship. To help these experimentalists and also beginners to MD to transcend the initial learning curve barrier of any MD simulation software, we developed a new tool that connects VMD to NAMD, two of the most popular simulation programs. Employing our tool, namely QwikMD, a user is able to setup a molecular simulation in just a few minutes, allowing for quickly study point mutations, partial deletions and even steering experiments. While making it easy for a new user to perform simulations, QwikMD also works as a learning tool with several "info buttons" where the theoretical background underlying the procedures is provided.

Incorporating the most widely used features of NAMD and VMD, QwikMD provides a graphical user interface (GUI) for the standard MD workflow (see image below). Built on this workflow, QwikMD automates all necessary steps while checking for common errors and ensuring reproducibility of the result by recording each step performed.

QwikMD Workflow

Spotlight: NAMD 2.12 Delivers Qwik, Quantum, and Cloud (April 2017)

NAMD Goes Quantum

image size: 507.7KB
made with VMD

The 2.12 release of the molecular dynamics program NAMD provides major enhancements in performance, flexibility, and accuracy, complementing the greatly enhanced usability provided by the QwikMD GUI released in VMD 1.9.3. NVIDIA GPU-accelerated simulations with NAMD 2.12 are up to three times as fast as 2.11, particularly for implicit solvent simulations and single-node simulations of smaller systems. NAMD 2.12 is also optimized for the new Intel Xeon Phi KNL processors found in Argonne Theta, NERSC Cori, and TACC Stampede 2. NAMD 2.12 builds on the asynchronous multi-copy scripting capabilities introduced in NAMD 2.11 with the ability to modify and reload the molecular structure, enabling development of grand canonical and constant pH ensemble methods, as well as an optional Python interface for advanced on-the-fly analysis. Finally, NAMD 2.12 provides a complete, no-recompilation-needed interface for hybrid QM/MM with both the semi-empirical code MOPAC and the ab initio/DFT code ORCA. More on new features in the 2.12 release of NAMD can be found here. NAMD is available free-of-charge as source code, precompiled binaries, pre-installed at supercomputer centers, and now jointly with VMD as one-click interactive molecular modeling on the Amazon cloud.

Other Spotlights

Support & Bug Report

The first version of QwikMD is available in VMD 1.9.3.

Attention, this is the first public release of QwikMD. Even though the software was exhaustively tested, QwikMD might still have some bugs so use caution.

If you find any problems using QwikMD please contact us by using our BUG REPORT form, or by e-mailing one of QwikMD's main developers: jribeiro@ks.uiuc.edu, rcbernardi@ks.uiuc.edu, or trudack@ks.uiuc.edu.

Any feedback is appreciated.

QwikMD Main Features

Easy Setup of MD Simulations

Point Mutations

Changes in Protonation

Protocols for MD, SMD, MDFF

Live View Simulations

Integrated Basic Analysis

Info Buttons to Guide Novices

Advanced Protocols for Experts

Setup Membrane Environment

Advanced Analysis

Full log Capabilities

Easy Reproducibility

Available on Amazon Cloud

Training & Workshops

QwikMD is an important part of our training workshops. You can check our upcoming workshops where your can learn more about Computational Biophysics here.

Documentation

QwikMD User's Guide

Development

QwikMD is in constant development by a team of investigators in Professor Klaus Schulten group at University of Illinois. The QwikMD main developers are:

Dr. João V. Ribeiro;

Dr. Rafael C. Bernardi;

Dr. Till Rudack.

How to use QwikMD?

For those who are experts in both Molecular Dynamics and Computational Biophysics, using QwikMD should be intuitive. For beginners, QwikMD is a perfect tool that helps overcoming the initial learning barrier imposed by most Molecular Dynamics software. The "info buttons" present in QwikMD help both beginners and experts to take the best advantage of Molecular Dynamics simulations. Each "info button" generates a window where the user can find fundamental information related to Molecular Dynamics simulations, such as the description of solvent models and protein structure, as well as short explanations of the options available in QwikMD graphical interface and the actions triggered by the buttons. For more information, the user is redirected to web-pages through links present in the bottom of the information window.

Please check out our one page tutorials, which are useful for a quick start. A complete tutorial is available on our tutorials website.

Download one page tutorials:

Scientific Successes

QwikMD is the newest software developed by our group and it was officially released in the Fall of 2016. However, QwikMD was already employed in some breakthrough research:

Making hybrid QM/MM simulations easy

Biomolecular force fields fail to address chemical reactions and other complex quantum effects near, e.g., reaction centers. Treating such parts of the molecule via quantum mechanics (QM), while the majority of simulation remains classical, allows the accurate representation of quantum effects in relatively large systems, such as enzymes. While many levels of quantum theory are available, QM/MM simulation requires the exchange of only positions, charges, and forces, enabling a common NAMD interface serving multiple QM engines.

In NAMD, a QM/MM interface to both ORCA and MOPAC has already been developed and is available in the nightly build of NAMD. QwikMD fully supports QM/MM simulations in VMD 1.9.4 (alpha) version.

Read more about QwikMD

1. QwikMD: Integrative Molecular Dynamics Toolkit for Novices and Experts; J.V. Ribeiro, R.C. Bernardi, T. Rudack, J.E. Stone, J.C. Phillips, P.L. Freddolino, K. Schulten; Scientific Reports, 6, 26536110 (2016)

2. NAMD goes quantum: an integrative suite for hybrid simulations; M.C.R.Melo, R.C. Bernardi, T. Rudack, M. Scheurer, C. Riplinger, J.C. Phillips, J.D.C. Maia, G. B. Rocha, J.V. Ribeiro, J.E. Stone, F. Neese, K. Schulten, Z. Luthey-Schulten; Nature Methods, (2018)

3. Easy and Fast Setup of Molecular Dynamics Simulations: Combining VMD and NAMD for Experimentalists; J.V. Ribeiro, R.C. Bernardi, T. Rudack, K. Schulten; Biophysical Journal, 110(3), 641a (2016)

4. Making Classical and Hybrid (QM/MM) Molecular Dynamics Easy and Fast with QwikMD; J.V. Ribeiro, R.C. Bernardi, T. Rudack, K. Schulten; Biophysical Journal, 112(3), 448a (2017)

5. QwikMD-Gateway for Easy Simulation with VMD and NAMD; J.V. Ribeiro, R.C. Bernardi, T. Rudack, K. Schulten, E. Tajkhorshid; Biophysical Journal, 114(3), 673a-647a (2018)