In case you want to perform a relaxed scan of the potential energy surface for a given dihedral, you have to perform constrained (or at least restrained) optimizations. The namd way to do so is to define a collective variable (colvar in namd terminology) and then impose a harmonic potential […]
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Some work is too boring to be done twice. In case anybody is interested in literature on experimental values for the densities of acyclic perfluoralkanes up to docosafluorodecane, here are some papers that might help. Please beware, as some of these publications are rather hard to find and contain partially […]
Daily backups are always a good idea – but sometimes a convenient accessible history is more helpful than having to work with raw database dumps. For I, Librarian backups are rather easy. This document describes the workaround necessary in order to introduce shadowing and change history for the database used […]
Sometimes, the list of entries on a single page gets very long. For quick navigation, you may either add a table of contents or collapse all content. In order to do so, add the following line to your layout.html template: {% set script_files = script_files + [pathto("_static/collapse.js", 1)] %} Now […]
Have you ever tried to spot a certain message in screens full of debugging output? Normally, you have a hard time scanning the text in order to find the output section you were looking for. Why not making the life easier for yourself (and your users) and start printing messages […]
If you’re not using autodoc, building a list of all your documented classes is not that straightforward. Unfortunately, sphinx does not offer any method to embed this list into your documentation. Below, you find a snippet that creates a sorted list of all classes. Here is what the result looks […]
In case you get an error message of the form FATAL ERROR: Setting parameter binaryoutput from script failed! you should try moving the line specifying the parameter in question in your config file. In particular, the parameter has to preceed any command actually performing calculations. For example, this config file […]
Although mendeley is convenient, it lacks proper support for documents created using version control systems like subversion. Usually, it is a bad idea to put the BibTeX file of the project under version control. Using the API of mendeley, there is way to Avoid duplicate entries with the same doi […]
Although usually it is helpful to define longer but explaining command line parameters, it will be tedious for users who work with this application very often to type out each and every parameter. Here is an example how to solve the problem for the python argparse module and choice options. […]
Everybody who owns a smartphone or a tablet has to think about the lock method of the device. Android offers an alternative to the usually used PIN code: the lock pattern. I have to admit that swiping fast and rather wildly over the screen is a cool way to unlock […]
During the dist upgrade from debian squeeze to wheezy, I got the following error from apt-get. E: Could not perform immediate configuration on 'gcj-4.7-jre'. Please see man 5 apt.conf under APT::Immediate-Configure for details. (2) The manual suggests to disable this method for dist upgrades. Googling suggests using apt-get dist-upgrade -o […]
If you get errors similar to the following ones: Paragraph ended before \@@href was complete. or File ended while scanning use of \@@href or output related to problems with \href@split, you should check your .bib file for entries like this Pages = {{2879-2882}}, In general, they are perfectly valid (although […]