Welcome to the CAMPARI home page!
We are proud to introduce the second official version of CAMPARI (v2).
Building on the stable platform provided by the original release (we have had to deal with comparatively few bug-fixes),
the new version adds a significant number of new algorithms, in particular in the
utilization of CAMPARI as a trajectory analysis tool.
For performing molecular simulations, we have refined and improved algorithms
on both the dynamics side (recursive algorithms for simulations in mixed rigid body and dihedral
angle space) and the Monte Carlo side (much better control over the set of degrees of freedom to sample
and the weights associated with each move type).
The largest change to the original version is the ability to perform simulations
for systems that are not contained in the internal CAMPARI residue database, and this change
coincides with many simplifications and generalizations at the code level.
It is our 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 (all functionality under the same hood), 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, AMBER94/99/03, OPLS-AA/L, or GROMOS53a5/6.
- 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
- Wang-Landau sampling in Monte Carlo simulations in energy or reaction coordinate space
- 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
- Implementations of recently published algorithms, e.g., tree-based clustering, J. Chem. Theor. Comput. 8 (3), 1108-1120 (2012), kinetic partitioning, Comput. Phys. Comm. 184 (11), 2446-2453 (2013), analysis of spatial density maps by equilibrium sampling, Structure 22 (1), 156-167 (2014), dynamics in mixed rigid body and dihedral angle space (manuscript under review)
- 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
- Domain-wise parallelization to speed up individual simulations
- Simulations of lipids and lipid membranes
- 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.