Macromolecular structure visualization: a look at the applications that provide graphical interface to structure analysis. Part V VMD.
The previous installments on these review series have focused on end-user GUI to 3D structure analysis and visualization. As I was getting ready to tackle the fourth I realized that the suite I wanted to review was actually geared towards molecular dynamics simulations. Thus, I took a detour into GROMACS territory. But now is time to actually review VMD. VMD stands for Visual Molecular Dynamics. Getting the most obvious out of the way, VMD runs on AIX, Linux, Mac OS X, Solaris and Windows. There are 32 and 64 bit binaries available. If you sport a fancy NVIDIA card you can also take advantage of GPU accelerated computing through CUDA.
NB I am a Mac user (10.6) and in the case of VMD (current version 1.8.7) I always run it through an alias via command line. That way the working directory is always the one where I invoke VMD.
VMD ease of use.
In the same fashions as in PyMol, Chimera or SPDBV, VMD has multiple interdependent windows for specific functions: the Main window gives you access to all of the other windows. Menus to control the way the visual window looks are in the Main window while the Extension Menus contain everything else use for trajectory analysis.
On the topic of trajectories and other files, the list of supported file is amazing, anything from AMBER, CHARMM, Sybyl, PDB, GROMACS, GROMOS, MMTK, .xplor, mrx, ccp4, brix… and more. Check VMD for the full list.
This window/menus organization is kind of difficult at first. However, it is very easy to get used to. Furthermore, using a .vmdrc file you can configure which windows pop up at first, their position or/and size.
Since VMD is a single app, independent from X11 or the terminal, it is easy to keep track of.
As mentioned before, if you have results from a molecular dynamics simulation then you can really take advantage from VMD (you can also use VMD to configure and run MD with NAMD). For example, there are very nice tools to get a plot of the number of H-bonds vs. time. Or, one of my favorites, you can get a cool Ramachandran 3D plot of the entire trajectory. Another good one is the salt bridge tool. I like this one because this tool allows you to select a group for salt bridge calculation. Other tools for the same purpose just go all out and calculate ALL salt bridges. Which is time consuming both for calculation and analysis. And, really, the list goes one. Most of these tools are easily accessible and configurable. There are a few that take some time to setup, just a few.
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| 3D ramachandran plot for PDB ID 1q9b. It sum up the data for a 50 ns simulation at 500K. |
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| VMD as I have configured the window size and position (.vmdrc). |
Overall strengths and weakness.
Distributed as a free binary download, VMD comes pretty much complete as it is. This is a big plus. There a few extra things you might need to download independently and configure afterwards. In don’t think I have done that myself but I wouldn’t expect to be that hard to do.
If you have to work on long projects, VMD offers the possibility of saving the state of your project.
My two complaints about VMD are that getting list of atoms or residues might be a bit difficult. And I am not talking about a graph with the sequences but getting a list (on demand) of residue id assignment, atom number and other identifiers. Sometimes quiet a few clicks are required to get that info.
The other is that atom/residue selection is a bit time consuming. Maybe I am just too dumb but having to type something like
same as residue within 5.0 of resname Zn
is a mouthful.
Conclusion.
Molecular dynamics are the gateway to function based on structure. Most MD packages include their own set of tools or enough info for a good programmer to setup software to do so. VMD provides quite a few powerful tools to do the same task. The advantage is that you will do that within a GUI environment. So, beside just clicking and little typing you can get to “see” the results in the context of the 3D representation of your system. This is actually very cool and can also give you good feedback for further analysis.
VMD is a good program to keep around for MD analysis.
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