Welcome to the CAMPARI gateway!

At long last, we have uploaded version 3 of CAMPARI to SourceForge, which means that you should navigate to the correct online documentation for the version you are interested in:

Take me to the documentation for version 2

Take me to the documentation for version 3

Note that no features, which were supported properly in version 2, have been removed in version 3. This means that there is little incentive to use version 2 at this point.
Version 2 will continue to be available but only critical bug fixes will be applied. Notably, an updated archive for version 2 has been uploaded as well: it differs by introducing a few minor extensions relative to the last uploaded version. The online documentation is current with regards to these changes but will in all likelihood receive no further updates. The aforementioned extensions are also part of version 3.
If you have never used CAMPARI before, we recommend to start at these two pages: If you have used version 2 before, you will probably most likely want to know what the biggest differences are and how they affect planned calculations. Overall, the major architectural change is the OpenMP support (see section on parallelism). Additional areas with significant improvements are the handling of PDB inputs (see documentation for FMCSC_PDB_READMODE), initial structure generation (see documentation for FMCSC_RANDOMIZE), and the performance of calculating nonbonded forces, The PDB parser is much more flexible and lenient so as to allow to work in conjunction with unedited PDB files obtained directly from the data bank (see the tool "convert_SEQRES_toseq.sh" in the tools/ directory in relation to this; a practical example is given in the revised Tutorial 6). Important feature extensions on the simulation side are support for the accelerated molecular dynamics method of Hamelberg et al. and the progress index-guided sampling method of Bacci et al.. In terms of parameters, we now provide access to CHARMM36 and derived parameter files for ABSINTH (abs3.1_charmm36.prm and so on). There is also built-in support for additional modified residues, e.g., acetylated lysine or phosphorylated serine, tyrosine, and so on (see sequence input documentation). On the analysis side, we have massively extended again the features collected under the structural clustering umbrella, e.g., to apply the increasingly popular time-lagged independent component analysis (tICA) or to calculate eigenvalue spectra and committor probabilities for Markov state models derived from structural clustering. All network/graph/MSM theoretical methods are now also available with a file-based supply of either a CAMPARI-external clustering or even starting from an ASCII file with the raw data (see documentation).
As before, note that links to source and other non-documentation files may not work in the web-version of the documentation. If you cannot find the file in question by hand, please refer to a local copy of the documentation obtained by downloading the package (here, all links should work).
Contributors - Links
Pappu Lab
Washington University in St. Louis, Missouri, USA
Website: pappulab.wustl.edu
Phone: +1 (314) 935-5416

Andreas Vitalis
Universität Zürich @ Caflisch Lab, Zürich, Switzerland
Current Website: biochem-caflisch.uzh.ch
Phone: +41 (44) 635-5568
Recent News

Sep 05, 2017
Official Release of CAMPARI version 3! As usual, check out the Sourceforge Page for further details and to keep up with bugfixes, additions, ongoing development, etc. Forums to request help, make suggestions, or report bugs are provided.

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