Visual Molecular Dynamics in Docker Container
The long-awaited new Ubuntu LTS Xenial Xerus was released last week. I wrote a tutorial on installing R and R-Studio on the old 14.04 LTS, so I figured I’d update that document. Not much has changed for the new 16.04 version but there are new repositories. You can find R-Base in the Software. Cd vmd-1.9.1./configure LINUXAMD64 cd src sudo make install Then type your password. The 'sudo' command tells your computer that you request to be allowed the permission to install the program into your computers default directory (e.g. /usr/local) when you run the next set of commands from the terminal.
VMD is designed for the visualization and analysis of biologicalsystems such as proteins, nucleic acids, lipid bilayer assemblies,etc. It may be used to view more general molecules, as VMD can readstandard Protein Data Bank (PDB) files and display the containedstructure. VMD provides a wide variety of methods for rendering andcoloring molecule. VMD can be used to animate and analyze the trajectoryof molecular dynamics (MD) simulations, and can interactively manipulatemolecules being simulated on remote computers (Interactive MD).
Why it was created?
This project is another quick and dirty solution to create VMD container almost from scratch.It compiles provided VMD sources and creates Debian package (*.deb) which is later installed in container.If you are planing to build VMD Debian package for distribution you should rather use vmd-debian project - it is better suited for deb package distribution.
Building VMD container image (Ubuntu host)
Starting VMD container (Ubuntu host)
Creating VMD container with home volume and X forwarding
Is it working?
Yes!
Tested VMD versions
- vmd-1.8.7.src.tar.gz - (md5sum: e8da2f2a5ffd5b4b2562eec77bbea8a3)
✅ - vmd-1.9.1.src.tar.gz - (md5sum: 661a3836df6598bad0bf15eca4d2f890)
✅ - vmd-1.9.src.tar.gz - (md5sum: ad52f695bdab5b94b860f82e88ed5c18)
✅ - vmd-1.9.2beta1.src.tar.gz - (md5sum: 799628156ae05cba7760772c71daa540)
✅
Other related projects
Additional references about Docker
License:
License Apache License Version 2.0, January 2004 (https://tldrlegal.com/ ; http://choosealicense.com/)
I have a remote compute server on which I would like to run VMD. Every time I start the application, it crashes with the following error report:
I heard from other users of the same server that they did not have any problems, so I assume this must be an issue with the X window system on my local machine.
Further points:
- I connect to the server using
ssh -X. - Opening a remote
xtermwindow works. - Local X windows version: 1.13.0
1 Answer
The X server on your system cannot support GLX graphics. You can confirm this using the following command:
I'd confirm that you have the necessary OpenGL and MESA drivers installed, since this application looks to require access to those libraries, looking at the VMD website it would appear to have somewhat demanding needs from your hardware. When I say 'your hardware' I'm talking about your local system, and not the one running the application, since your system is responsible for driving your local display.
CUDA?
In looking through the VMD website I did find this page, titled: VMD CUDA Acceleration Notes which sounds like it might be related to your particular warning messages as well, if you're curious to get rid of those. Also there is a message on that page that states: 'VMD requires NVIDIA GPUs that support CUDA'. A list of CUDA capable NVIDIA cards is also available.
BadAlloc
These messages would seem to be implying that your local video card does not have enough resource (GPU RAM) I would assume.
You might be able to get around this by reducing the size of your desktop display, potentially as well. You should be able to do this through your distro's control center, typically under the 'Displays' applet. That's where it would be with a GNOME 3 type of desktop.
What Graphics do I have?
You can use the following commands to find this information out.
Method #1 - lspci
Now we know the device ID (02.0) so we can use this to get additional information.
Method #2 - hwinfo
Method #3 - lshw
