getting trusted with ever more expensive equipment...

...this time a SEM. I finished up my qualifications for "limited supervision" use of a SEM at Michigan State Thursday. Basically I can use it as long as there is a guru at least in the building, so normal business hours. I had planned to wrap this up a couple of months ago, but right after my second training session the scope went down and then a slew of scheduling problems. The down time had nothing to do with me, despite the rumors, but something about turning off the air conditioning for season.



BSD mode


Now to sweet talk my way on to the TEM and AFMs

getting atom trajectory files from GROMACS

What I mean by atom trajectories is the xyz coordinates of each atom at each time step. I could not find any program in the gmx package that did this, so I wrote my own. You can get it here.

From gromacs, use the trjconv program to create a series of pdb files for each time step of the simulation.

trjconv -s swnt -f traj.trr -o last.pdb -sep

swnt is the structure, traj is the trajectory file created from running a dynamics simulation and last.pdb is the name you give to the pdb series.

After running the script you get a text file for each atom the has the time and xyz coordinates:

Here is a sample output for atom 1

convert protein data bank files into Ansys nodes, key points and lines

Here are two small python scripts I wrote that will read in a PDB file and output a text file to be used as input for Ansys finite element analysis. They're still kind of rough in that the input directory is hard coded, but they seem to work great at least for carbon nanotubes and other fullerenes.

convert PDB file to Ansys key points and lines

convert PDB file to Ansys nodes



To use these scripts:

1. create a protein data bank file of your structure
2. name it test.pdb and save it in a folder: C:\xyz
3. make sure you have python installed
4. and to make things easier for development and use, grab the free version of Wingware IDE 101
5. download the two scripts and open them in Wing
6. run the scripts


The output file will be in the xyz directory. To load them in Ansys: File > Read input from...

carbon nanotube NEM animated in Blender

This is a version that won't be used, so I decided to post it here. I'll post a flow chart on how to visualize actual dynamics data in Blender when I get back. It has all the steps, but not all the steps are finished yet on my end. Maybe it will be a good stroy arc.

molecular rotor animation rendered in Blender

I think blender can be a very useful tool for scientific visualizations, particularly with respect to visualizations of molecular dynamics simulations. There's a couple of missing steps as far as I can tell, but I'm working on them and will save that for the next post. However if you just want to make some eye candy, you can pretty much dive right in. This is a good example of something I've come to understand: modeling stuff is easy, the tricky part is making those models represent something relevant.

free stickers!

I came up with this a while ago as a purposed emblem of a certain sub-culture that, if you're reading this, you may belong to. I don't want it to go to waste, and I'm not even a bumper sticker guy. Email me a mailing address, and when I get a good collection I will send them out. Or you could always make your own, but that's not really the same, is it?

molecular gear published in Nature Materials

Step-by-step rotation of a molecule-gear mounted on an atomic-scale axis
C. Manzano1*,W.-H. Soe1*, H. S.Wong, F. Ample, A. Gourdon, N. Chandrasekhar and C. Joachim1,2

compared to the small bearing (disassembled) of old: