On some rare occasions you might wonder how a certain energy term shapes the energy landscape of your molecule. Adun let’s you play with the forcefield turning on and off each of the energy terms during a simulation through the use of AdunShell. Let’s see how to do it First you create the template for [...]
For the first time, developers of Adun are meeting in Barcelona (UPF Ciutadella Campus, seminar room 13108 1st floor R.Turró building) to discuss recent improvements on the code, propose improvements and to share common development rules. The first Adun developers meeting (ADM 2010) is going to be held at the UPF communication campus (Edifici R. [...]
Two new guides are available in the documentation section. The first details Adun’s user customizable preferences. The second describes how to set up and test Adun’s experimental P2P database sharing technology.
Release notes for v0.81 These are the release notes for version 0.81 of the Adun molecular simulator. It’s been a while since the last release, and in addition to the changes listed below v0.81 contains fixes for far too many bugs to mention, and numerous small user tweeks. The new version also sees assorted changes [...]
The guide answers some FAQ about scripting with Adun and contains short examples of using it via Adun’s interactive shell. This is a preliminary version of this guide and it will be extended with further examples, including full scripts, in the coming months. Scripting features were added as standard to Adun in v0.81, which is [...]
The first Mac version of Adun is available through our download page. It is compatible with OS X 10.4+. This version is less stable than the linux equivalent since it has undergone less testing, however it is functionally identical. Once you download the dmg it will open to show two packages – install Adun-0.74 first [...]
This plugin calculates the native contacts in protein chains, returning a table of the contacts in each chain plus the contact order and a contact map. It can take pbds, adun systems and adun simulations as input. It can also calculate the fraction of native contacts in a second structure relative to the first. Again [...]
First releases of MultipleAlign, RMSDMatrix, Correlation & Superimpose plugins are available here. These plugins are only compatible with v0.8rc and higher. Once the official 0.8 release is made entries will be added for these plugins on the plugin download page. For now see these announcements for more information – Superimpose & Correlation RMSDMatrix MultipleAlign In [...]
The RMSD update brings increased speed. The EssentialDynamics plugin now checks that a supplied reference system has the same number of analysis atoms as the trajectory system e.g. the same number of C-Alphas for a C-Alpha only analysis. Previously it checked the contents were exactly the same. This meant that if e.g. a hydrogen was [...]
