vmd

About

From the VMD project page:

VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

Versions and Availability

Module Names for vmd on qb2
Machine Version Module Name
None Available N/A N/A
▶ **FIX-ME** FAQ?

Usage

VMD is an interactive X-Windows application, so you will need to to make sure your SSH session, and have an X-Windows server running on your local machine.

▶ X11 FAQ?

From *nix

Since ssh and X11 are already on most client machines running some sort of unix (Linux, FreeBSD, etc), one would simply use the following command:

% ssh -X -Y username@remote.host.tdl

Once successfully logged in, the following command should open a new terminal window on the local host:

% xterm&

An xterm window should appear. If this is not the case, email us.

From Mac OS X

An X11 service is not installed by default, but one is available for installation on the OS distribution disks as an add-on. An alternative would be to install the XQuartz version. Make sure the X11 application is running and connect to the cluster using:

% ssh -X -Y username@remote.host.tdl

From Windows

Microsoft Windows does not provide an X11 server, but there are both open source and commercial versions available. You also need to install an SSH client. Recommended applications are:

  • Xming - a Windows X11 server
  • PuTTY - a Windows ssh client

When a PuTTY session is created, make sure the "X11 Forwarding Enabled" option is set, and that the X11 server is running before starting the session.

Testing

Once Xming and puTTY have been set up and in stalled, the following will provide a simple test for success:

  1. start Xming
  2. start puTTY
  3. connect to the remote host (make sure puTTY knows about Xming for this host)

Once successfully logged in, the following command should open a new terminal window on the local host:

% xterm&

An xterm window should appear. If this is not the case, refer to "Trouble with Xming?" or email us.

Note About Cygwin

Cygwin is still a useful environment, but is to complicated and contains too many unnecessary parts when all one wants is to interface with remote X11 sessions. For these reasons, we recommend Xming and PuTTY as listed above.

Advanced Usage

The most important connection that is made is from the user's client machine to the first remote host. One may "nest" X11 forwarding by using the ssh -XY command to jump to other remote hosts.

For example:

1. on client PC (*nix or Windows), ssh to remotehost1

2. on remotehost1 (presumably a *nix machine), ssh -XY to remotehost2

3. on remotehost2 (presumably a *nix machine), ssh -XY to remotehost3

...

8. on remotehost8 (presumably a *nix machine), ssh -XY to remotehost9

9. on remotehost9, running an X11 application like xterm should propagate the remote window back to the initial client PC through all of the additional remote connects.

The application is then started in the usual fashion:

    $ vmd [options] filenm
  

The -h switch can be used to list the allowed options.

Resources

Last modified: July 06 2015 14:34:42.