Machine Phase

Installing GROMACS 5.0.4 on Ubuntu 14.04 using cmake

2015-05-04T10:49:00.000-07:00

Install necessary packages:

sudo apt-get install cmake

sudo apt-get install build-essential

sudo apt-get install libboost-dev libxml2-dev

sudo apt-get install libfftw3-dev libfftw3-doc

1. download gromacs source gromacs-5.0.4.tgz

2. cd ~/Downloads

3. tar -xvzf gromacs-5.0.4.tgz

4. mkdir build

5. cd build

6. sudo cmake .. -DCMAKE_C_COMPILER=/usr/bin/gcc -DCMAKE_CXX_COMPILER=/usr/bin/g++ -DGMX_BUILD_OWN_FFTW=ON

7. sudo make

8. sudo make install

Been a while

2012-01-12T13:10:00.000-08:00

Quick MD simulation done in SIESTA and visualized in VMD. I have a back log of stuff to post, but I might move on to the new stuff.

pillared graphene

2010-09-09T06:41:00.000-07:00

Small molecular dynamics simulation carried out in GROMACS and visualized in Blender as part of a larger project I'm still working on.

Rolling my own part two

2010-05-29T22:27:00.001-07:00

The version numbers could be a little nuts here for a while. I probably won't post anything else until they get into double digits as I can't imagine this is interesting to anyone but me. The major improvement here is the ability to distinguish different atoms in the input file and draw them accordingly. The radii still need a little adjusting.

Rolling my own

2010-05-25T20:18:00.001-07:00

Reading in xyz coordinates and rendering them in PyOpenGl

I figure by the time I'm done it will be best-in-class, export controlled and retail for a couple hundred thousand dollars. You saw it here first.

Oh yeah, I can rotate and zoom the camera using the mouse. Jealous?

Scripting atom color changes as a function of velocity in Blender

2010-05-24T16:15:00.000-07:00

Atom colors change as a function of their velocity using the basic how-hard-is-it-raining convention, slower is blue, white is pouring. RGB values for individual atoms were calculated from molecular dynamics data and imported as object color IPO curves. For this I expanded Miron's import IPO script to include three more curves, one for each RGB.

I plan to develop this more to represent temperatures.

Diamond Bearing

2010-05-19T19:31:00.000-07:00

I obviously have a small glitch in importing these models from NE1 to Blender in that I lose a single atom. I bet it is either the first or last.

For a beautiful version of the same structure check out Euplotes'
He has lots of other good stuff too.

Atomistic Large Bearing: dynamics performed in NanoEngineer-1, vizualized in Blender

2010-05-09T18:15:00.000-07:00

The initial visualization of 550 frames, skipping two simulation steps at 50f/s, motion blur set 0.5 averaged over 5 frames. This took about 20 hours to render on a basic core 2 duo notebook.

9 frames, skipping 100 frames looped, motion blur set to 5 averaged over 16 frames. About 20 minutes per frame to render.

C60 fullerene melting

2010-05-03T15:31:00.000-07:00

Atomistic Small Bearing: dynamics performed in NanoEngineer-1, visualized in Blender

2010-04-28T16:33:00.000-07:00

The astute viewer will notice two things first:
1-I still can not frame a shot for shit.
2-The back side of the rotor is missing a hydrogen atom

Well, these are still more or less movies where I am more concerned with getting different things to work than I am with cinematography and such. Maybe next time I'll throw in some long parallel walls to frame the action. Also any long time readers of this site will know that I have had my problems with hydrogen in the past, but, all in all, things have come a long way from the last time I posted anything about the famous small bearing first proposed by K. Eric Drexler back in 94, I believe.

A little about how I did it:

NE1 will save simulations in two ways, either as a binary file (which I can't do much with right now expect turn into gibberish) and a series of POV-Ray files, one for each time step. So you are probably thinking "why not just stitch the povs together, adjust the lighting, camera, materials, whatever and call it a day?" I know POV-Ray is great, and I'm pretty sure it is all Pixar uses, but I'm just a gui type of guy I guess. So I have written a Frankenstein's Monster of a script that will read in a series of povs and create atom trajectory files, one for each atom. Normally it would then just be a matter of using Miron Cuperman's import_ipo_script to connect the atom trajectory files with a PDB model which NE1 exports and Miron has also provided a very fast importer for.

The only problem here is NE1 writes the atoms in a different order in povs and PDBs. It is very important that the right trajectory matches up with the right atom. So I added another section (subroutine?) to my script that will read in the first pov ray file and create a bona fide .xyz chemical format file. I went with the .xyz because it is the simplest format I know of. Then all you have to do is run it through Open Babel to convert it into a PDB file that has the same atom order as the pov files and can be imported into Blender. That's all there is to it.

I fully intend to clean it up, rewrite parts so they're not embarrassing (even for me) but if you can't wait, you can get a copy of my ne12blendXXX.py script. The XXX stands for a couple of things. Guess!

C60 and C240 collision at 300eV

2010-04-27T15:58:00.000-07:00

Related:

C60 and C240 collision at 10eV

C60 and C240 collision at 10eV

2010-04-23T13:31:00.000-07:00

Something a little more than just jiggling

This would not have been possible without the help of Miron Cuperman and his coding skills. Miron has written a nice python script to automate the process of importing csv data in Blender to animate objects. You can get a copy here

I will be the first to admit I am far from a Blender pro, but I hope to be able to show off some of the features that other visualizers don't have or do in a way I find cumbersome. This episode: Camera Tracking

More interesting stuff is on the way too.

MTF

fullerene capsule: molecular dynamics performed in GROMACS, visualized in Blender

2010-04-13T19:57:00.000-07:00

and one more, why not?

Can you put it in a wine glass?

2010-04-11T12:20:00.000-07:00

Sure

C60 fullerene- molecular dynamics performed in GROMACS, visualization done in Blender

2010-04-10T19:30:00.000-07:00

visualizing GROMACS simulations with Blender (teaser)

2010-04-08T18:16:00.001-07:00

This was a proof of concept test, so I'm not going into the details of how to do it right now. There are also a couple of steps I still need to automate to make this a practical solution; that's why there is only five atoms in this one. However I'm optimistic those can be worked out easy enough. After that I'll upload a turn-key script of sorts that will give you the features and flexibility of Blender to render GROMACS molecular dynamics simulations.

Related:
Atom Trajectories from GROMACS
Carbon Nanotube Animated in Blender
Molecular Rotor Animated in Blender

MTF

Carbon Nanotube Manipulator Concept

2010-03-13T17:16:00.000-08:00

Branched carbon nanotubes have been in the literature for a while now* and make up the business end of this manipulator concept. The idea was inspired by a wire grasper out in the garage. The macro-scale version looks something like this:

The way I picture the nanotube version working is a little different in that instead of the grasping fingers retracting in, the cnt version would use electrostatic forces to extend the outer carbon nanotubes over the branched tube. This lowers the chance that the fingers slip off whatever is being grasped. This would also require the inner-most tube to be anchored.

MTF

*Branched carbon nanotube junctions predicted by computational
nanotechnology and fabricated through nanowelding
,D. Srivastava, M. Menon and P.M. Ajayan,
Journal of Nanoparticle Research 5: 395–400, 2003.

getting trusted with ever more expensive equipment...

2009-12-18T17:58:00.000-08:00

...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

2009-12-18T09:27:00.000-08:00

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

2009-11-30T20:14:00.001-08:00

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

2009-08-23T17:55:00.000-07:00

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

2009-08-22T23:53:00.000-07:00

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!

2009-08-16T19:25:00.000-07:00

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

2009-06-22T21:40:00.000-07:00

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:

riding the rails

2009-06-13T22:05:00.000-07:00