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I made a short tutorial on installing and using ipython parallel in a ipython notebook. As it is an ipython notebook itself, please follow this link.
Sometimes, it may be helpful to select a Drupal 6 theme depending on the domain being used for every request. Although there are full-fledged solutions like Domain Access, they may be considered overkill for this problem. A reliable and quick solution is a custom module which is also compatible to […]
When using the Linux Libertine font family on MacOS, everything is fine with LaTeX, as the MacTeX distribution already includes all relevant files. In case you use third-party tools like Inkscape, you will have to install the font files which is a bit different from what Linux users are used […]
When using TotalTerminal, a guake-like terminal helper, the default shell, bash, is not started under execution of the .bashrc. Hence, any custom commands defined or changed in this file will not be effective until you source the .bashrc manually.
Embedding one molecule (e.g., a protein) into another one (e.g., a membrane) has to be done carefully in order to avoid any conformational clashes. For the GROMACS world, there is g_membed, but for namd there is no tool that I know of. So here is a TCL script to help […]
When transferring pen-and-paper calculations into computer code, issues related to floating point precision tend to arise. For my preferred rapid prototyping language, python, this is the case as well. Of course, you can work with the decimal module, but this does not help you out in each and every case. […]
When using the tclBCScript interface of namd for imposing additional forces on a classical molecular dynamics simulation, you may get the (undocumented) error message ------------- Processor 0 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: tclBCScript failed to call nextatom until failure Charm++ fatal error: FATAL ERROR: tclBCScript failed to call […]
In case you use your I, Librarian database together with BibTeX, you will most probably will be annoyed by the recurring task to export your current literature database to a bibfile. Here is a short script that dumps all entries from a I, Librarian instance to your command line. So […]
This short article will guide you through the creation of images like the one above based on charge density calculations using Gaussian09. For visualization, I will use Jmol. The principal steps are: Get a conformation of the molecule you are interested in. Optimize this geometry until you find a local […]
In case you get something along the lines of $ formchk input.chk output.fchk Read checkpoint file input.chk Write formatted file output.fchk Missing data for FChkPn. Error termination via Lnk1e at <DATE> Segmentation fault this means that your checkpoint file (*.chk) is damaged. Please make sure, that … … you have […]