VMD

A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Bernd Kallies⁽¹⁾

Revision History:
Revision 1.2, Published 2006/11/14 20:26:57 (UTC) by Bernd Kallies

Table of Contents

1. General Information
2. Functionality
3. Online Documentation
4. Usage Conditions and Licensing at HLRN
5. Details of the HLRN Installation of VMD
6. Getting started

1. General Information

Version: VMD 1.8.5 (Oct 2006)

Vendor: Theoretical Biophysics Group at the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA.

2. Functionality

Please visit the following links for detailed informations:

3. Online Documentation

VMD 1.8.5 User's Guide (HTML, PDF)
VMD Script Library

4. Usage Conditions and Licensing at HLRN

The software VMD is intellectual property owned by The Board of Trustees of the University of Illinois on behalf of The Theoretical Biophysics Group in the Beckman Institute.

The Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) holds a restricted, non-exclusive, non-transferable license to use the software for academic and research purposes. ZIB provides access to the binaries of the software to users of the HLRN, which understand and agree to the terms and conditions of the License Agreement.

Any reports or published results obtained with VMD have to acknowledge the use of VMD by the appropriate citations as follows:

VMD was developed by the Theoretical Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.

Any published work which utilize VMD shall include the following reference:

Humphrey, W., Dalke, A. and Schulten, K., VMD - Visual Molecular Dynamics, J. Molecular Graphics, 1996, vol. 14, pp. 33-38.

5. Details of the HLRN Installation of VMD

The current VMD version installed is 1.8.5 (for AIX5 64bit, uses OpenGL).

5.1. Installation Path, Environment

The current installation path to the binaries is /aws/chem/vmd-1.8.5/bin. The executable is started by the command vmd. We provide a VMD module file that appends this path to the $PATH variable, and sets several other VMD-related environment variables.

Add the following command to your ~/.profile (ksh users) or ~/.cshrc (csh users), if you plan to use VMD:

module load vmd

Execute the command module avail to see a list of all provided module files. There may be previous VMD versions installed, which are not mentioned here. Please read Environment in The HLRN Quickstart Guide to learn more about the modules package.

6. Getting started

After loading the vmd module file, start the GUI with vmd. Look into the User's Guide for further information.

In order to work with the GUI, you have either to

enable X11 forwarding for your ssh connection, e.g. by using ssh -X berni.hlrn.de.
disable X11 forwarding for your ssh connection, set the DISPLAY variable appropriately after logging in into a HLRN machine, and allow remote X11 connections to your local machine. This may be done e.g. by
```
> xhost +berni1.hlrn.de
> ssh -x berni.hlrn.de
$ export DISPLAY=your-machine:0.0
```

Enabling X11 forwarding should work in any event, if ssh works. However, this may be slow depending on the speed of your internet connection and your local machine.

If working without X11 forwarding will work or not, strongly depends on the configuration of your local machine or site (ssh and firewall configuration). See HLRN-FAQ-566 for additional hints. Contact your local administrator if you have problems.