Friday, December 18, 2009

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