VMDMagazine

Operating systems: Windows, MacOS and Linux.

Contacts : Nuno Sousa Cerqueira Pedro A. Fernandes Maria João Ramos

Visualization can be a motivating way of teaching students about the microscopic world. This can become even more exciting if the information is based on accurate computational results rather than on crude approximations that eventually might create unreal alternative perceptions. Here, we report on a VMD plug-in – VMDMagazine, which can play and handle computational simulations into stunning high-impact video presentations, suitable for classes/lectures and even conferences. The software will help students/audience to understand atoms and molecules better and learn to like them.

VMDMagazine was developed with the goal of visualizing scientific information without requiring any prior knowledge of the user in the area of molecular visualization or even molecular modeling. This means that the users (teachers and students) do not have to worry about the handling of molecular visualization software or in the preparation of such types of visualizations that normally involve complex selection steps and the upload of multiple files and scripts.

All the images/Movies handled by VMDMagazine can be easily built under the VMD environment and it only requires the upload of a structure, the modification of the atoms representation and save the vmd session and associated files into a custom directory. Later, the user can add a subtitle to the image/movie by the creation of a simple txt file in the same directory. All these procedures are very simple and almost every one should be capable of doing them, even those ones that have less experience with the VMD interface.

As VMDMagazine only requires the VMD software it can be used in any platform where VMD can be used, i.e., plataforms that run the windows Os, MacOs and Linux Os.

In order to run the VMDMagazine plug-in, the Visual Molecular dynamics software (VMD) must be installed. The installation of NAMD ( molecular dynamic simulation program) is optional.

VMD can be found at http://www.ks.uiuc.edu/Research/vmd/ .
NAMD can be found at http://www.ks.uiuc.edu/Research/namd/ .

The VMDMagazine plug-in runs in any platform where VMD runs, i.e., Windows, OSX and LINUX.

1. Install the VMD software ( if you haven't installed it yet).
2. Extract vmdMagazine.zip file to your Desktop directory.
3. Open VMD and open the tk console that can be found in the Extensions menu (last item).
4. In the tk console go to the directory where the vmdMagazine was extracted and run the installer. Then enter the following commands:

   cd                     <Enter>
   cd Desktop             <Enter>     Note: (a)
   cd vmdMagazine_v1.0    <Enter>
   play install.tcl       <Enter>

1. Follow the instructions of the installer. (b)
2. When the installation is complete, exit the VMD program and open it again.
3. Once this procedure is complete the vmdMagazine plugin can be found at the VMD extensions menu (CompBioComp»vmdMagazine).

Important: On windows OS the VMD might have to be started with administrator privileges.

Notes:

(a) In this case the vmdMagazine package was extracted to the Desktop directory. In windows OS this directory can have other names. For example in portuguese it is called Ambiente de Trabalho. Therefore the command that is used should be: cd Ambiente de Trabalho.

(b) The NAMD executable is optional and it is only required to run the files that run interactive simulations.

The vmdMagazine Database provides several examples that can be used with the vmdMagazine plug-in to explore the chemical/biochemical microscopic world.

To access the vmdMagazine Database click on the image below.

1. Download the zip file to the computer.
2. Extract the files to the directory that is read by the vmdMagazine plug-in (this can been seen in the Options window of the plug-in), or extract the files to a new directory. If the last option is used, do not forget to point the vmdMagazine plug-in to that directory, in order to see the contents of the package.

In the next file some instructions are given that can be used to create new VMDMagazine packages. The authors can send an email to nscerque@fc.up.pt to include the developed packages in the VMDMagazine database.

Tutorial: createnewvmdmagazinepackages.pdf

Video 1 : Tutorial of vmdMagazine.

Video 2 : vmdMagazine with a 3D television and a Novint Falcon Joysticks used in “Dia aberto da Química da Universidade do Porto”, May 2013