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All posts in one place
I finally decided to consolidate all my old posts from the past two blogs in one place. There weren't many posts and the migration was painless. Thanks to Github and Jekyll, creating a static blog was very easy too!
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PyMol and OSX 10.8
Here are some quick notes on installing PyMol in OSX Mountain Lion using MacPorts:
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Compiling VMD with Python 2.7 and CUDA 5.0
No, it’s not an April fool’s joke. And yes, it wasn’t easy to do!
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And let there be Python
If you do some sort of molecular modeling, you almost certainly used one or more scripting languages to make your life easier. I’ve tried some of them and my favorite by far is Python. Other than being very readable and having simple syntax, one thing that especially makes Python very useful, is myriad of available modules that enhance the core functionality. For example you can use Numpy to do fast numerical analysis, Scipy to do linear algebra calculations, mathplolib to plot your data, MDAnalysis to analyze your simulation trajectories or use Prody to do GNM calculations.
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How to compile GromacsGUI 0.5.x
This is a mini-howto for compiling GromacsGUI mainly for those who may have not worked with compiling stuff before, or want to test the software in linux distributions other than (k)ubuntu 8.04 and OpenSuse 10.3 for which I explained exact steps.
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How to compile GroGUI 0.5.x in (K)ubuntu 8.04 and OpenSuse 10.3
(K)ubuntu 8.04
- Use Adept and install these packages:
g++, make, libqt4-gui, libqt4-dev, libqwt5-qt4, libqwt5qt4-dev.
- Use Adept and install these packages:
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I love dynamics!
Long time from my last post! Quite busy these days, I actually can not find any free time. Now I am at surgery ward, in which the daily work starts at 6:00 AM until 11:00 AM, and we usually have 12 shifts per month. Besides, work from my thesis, GRE exam, my applications to universities and some minor things (like the lecture I have to present this Monday about diabetics foot) fill any minute amount of free time. However, I see all these businesses as the dynamics of life (although I think the kinetic energy of my dynamics is relatively high!) and like my scientific interests, I love dynamics!
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Version 0.5 beta released
After about one month of development, now the version 0.5 is ready. I also prepared an introduction slideshow which was created using wink.
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News
After about 4 weeks of looking, learning, thinking and writing code, and again looking, learning, thinking and writing code, and again… now I’ve learned Qt enough to find my way. Coming from python world, it was relatively difficult to get accustomed with “new” and “delete” especially when working with raw data! The plotting tool has been more matured. As I said before, I delayed molecular viewer part to the next major release (I hope it to be developed in coming months). Nevertheless, just for my curiosity, I wrote a simple “test” viewer using OpenMOIV and also played a little with BALLView. The results were promising.
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Exhausted...
I have been recently busy with some coding. About 2 weeks ago, while working with GROMACS using my small Gromacs GUI app, I found that it was time to add some new features . I decided to rewrite it all over, but this time in Qt4. Python provides a simplified way to write your code, but I think using C++ with Qt flavor can be a real good alternative.
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Fars
My family currently live in Shiraz, Fars province. A beautiful landscape of Fars from wikipedia.
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So It Starts...
After some searching about blog providers, I finally chose WordPress over others. And so my blogging experience starts… .
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