Monday, May 4, 2015

Installing GROMACS 5.0.4 on Ubuntu 14.04 using cmake

Install necessary packages:

sudo apt-get install cmake
sudo apt-get install build-essentials
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

Thursday, January 12, 2012

Been a while


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.

Thursday, September 9, 2010

pillared graphene

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

Saturday, May 29, 2010

Rolling my own part two

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.

Tuesday, May 25, 2010

Rolling my own

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?

Monday, May 24, 2010

Scripting atom color changes as a function of velocity in Blender

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.

Wednesday, May 19, 2010

Diamond Bearing

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.