Welcome to the CAMPARI home page!

We are proud to introduce the third official version of CAMPARI (v3). This version of CAMPARI differs dramatically from its predecessor, as most functionalties of the code can now benefit from an OpenMP threads parallelization. Given that modern computing resources routinely feature tens of cores in a single shared memory node, this change means that CAMPARI can now also be employed for simulations of larger, dense systems while maintaining a reasonable production rate. In addition, some of the inner loops (mostly for gradient-based propagators) have become faster by factors of 2 or more even when executed just by a single thread. Because of our development model, CAMPARI does not strive to compete with pure performance-optimized codes like GROMACS, but rather maintains its prior philosphy, that is, to rigorously support and maintain a wide array of methods and analysis tools "under the same hood."

It is our continued hope that the tools we provide for the molecular simulations of biological macromolecules and their analysis can be as useful to other users as they are to us. We believe that CAMPARI populates a relevant niche due to its unusual layout, internal structure (explicit and system-specific support for biological macromolecules at many levels), the wide class of supported algorithms, its extensive documentation (including tutorials), and the reference implementation of the ABSINTH implicit solvent model and force field paradigm.
If you are new to this software and/or this documentation, please refer to the documentation overview page. From there, you will be able to obtain an idea of the basic workings of CAMPARI, and you will be directed to the remainder of the comprehensive documentation. Note that a few links may not work in the web-version of the documentation found at campari.sourceforge.net. In that case, please refer to a local copy obtained by downloading the package.

Some of the features built into CAMPARI include:

Features Supported by CAMPARI:

  • Flexible Monte Carlo sampling of biopolymers in internal coordinate / rigid-body space
  • Minimization and dynamics-based sampling (MD/LD in NVE/NVT) in internal coordinate / rigid-body space
  • Cartesian space minimization and dynamics-based sampling (MD/LD in NVE/NVT) including support for custom sets of holonomic constraints
  • Hybrid sampling algorithms combining Monte Carlo and dynamics methods
  • Ported parameters and paradigms for major force fields such as CHARMM22/27/36, AMBER94/99/03, OPLS-AA/L, or GROMOS53a5/6
  • OpenMP-based shared memory parallelization of all supported samplers (with the exception of some Monte Carlo move sets)
  • Full support and control of the ABSINTH implicit solvation model and underlying force field paradigm
  • Near-complete control over Hamiltonian through tuning of intrinsic parameters via simple keywords
  • Simulations of arbitrary systems based on 3D input geometries by means of extensive patch facilities to all energy terms
  • Support for droplet and periodic boundary conditions with standard long-range electrostatic corrections such as particle-mesh Ewald or reaction field methods
  • Very wide support for replica-exchange simulations (available in multidimensional form in Hamiltonian space) with explicit support for free energy calculations
  • Hybrid MPI/OpenMP parallelism for multi-replica simulations: inter-replica communication via MPI and speed-up of individual replicas by OpenMP
  • Full support for the Progrss Index-Guided Sampling (PIGS) method
  • Wang-Landau sampling in Monte Carlo simulations in energy or reaction coordinate space
  • Support for sculpting of energy landscapes (commonly known as "accelerated molecular dynamics") for all samplers
  • Different biasing potentials to global secondary structure content, polymeric properties or to individual geometric variables
  • Support for arbitrary tabulated potentials (spline-based) and density restraints (spatial)
  • Molecule builder for polypeptides, polynucleotides, and various small molecules without the requirement to provide any structural or geometric input
  • Built-in analysis routines pertaining to polymeric properties (e.g., simulated scattering data), structural properties (e.g., secondary structure assignment for polypeptides according to DSSP), solution structure (e.g., arbitrary pair correlation functions), and many more (with the ability to perform these analyses "on-the-fly")
  • Various clustering algorithms operating on a large selection of possible coordinates
  • An entire toolkit dedicated to network (Markov state) models and their analysis (committor probabilities, steady states, etc.)
  • Implementations of recently published algorithms, e.g., for data mining, tree-based clustering, J. Chem. Theor. Comput. 8 (3), 1108-1120 (2012), kinetic partitioning, Comput. Phys. Comm. 184 (11), 2446-2453 (2013), automatic feature selection, J. Chem. Theor. Comput. 11 (11), 5481-5492 (2015); for simulation methodology, analysis of spatial density maps by equilibrium sampling, Structure 22 (1), 156-167 (2014), dynamics in mixed rigid body and dihedral angle space, J. Chem. Phys., 141 (3), 034105 (2014), or the progress index guided sampling method, Biochim. Biophys. Acta, 1850 (5), 889-902 (2015).
  • Conversion of various binary trajectory file formats and PDB naming conventions, program execution in trajectory analysis mode (also in parallel)
  • Completely free and released under the GPL

Features currently not supported by CAMPARI but commonly found in other simulation software packages:

  • Implicit solvation models other than ABSINTH or primitive models
  • MPI-based "classic" domain decomposition for dense systems (see OpenMP functionality above)
  • Sampling of constant-pressure ensembles using manostats

The above lists should provide you with a good idea of whether CAMPARI may be a useful addition to your toolkit. The list of references contains many examples of research performed with the help of CAMPARI.
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) 635-5597
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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