CAMPARI History

The primary developer of the software CAMPARI and the implicit solvation model ABSINTH is Andreas Vitalis. CAMPARI was developed during stays in the lab of Rohit V. Pappu at Washington University in St.Louis, USA and in the lab of lab of Amedeo Caflisch at the University of Zurich. The first, second, third, and fourth versions were released in 2010, 2014, 2017, and 2020, respectively, and the current version (5.0) was released in 2024. The CAMPARI development team is indebted to many scientists having developed and implemented algorithms into software such as GROMACS, CHARMM, or TINKER for inspiration.
Funding during this time was provided by several grants to Rohit Pappu (grants from the National Science Foundation, such as MCB-0416766 and MCB-0718924 from 2004-current, and grant 5R01NS056114 from the National Institute of Health from 2007-2020). Funding for Andreas Vitalis and, partially, other developers during the relevant time came from grants of the Swiss National Science Foundation to Amedeo Caflisch, a grant from the Platform for Advanced Scientific Computing (PASC), and personal grants (to AV) from the Forschungskredit of the University of Zurich and the Holcim foundation.

CAMPARI Support

In 2024, a list of current and past CAMPARI developers contributing to this release is as follows (alphabetical order):

1. Marco Bacci, Ph.D.
   Primary user experience: Hybrid dynamics/Monte Carlo simulations, PIGS, spatial density restraints, clustering, SAPPHIRE plots, Markov state models
   Development: Markov state models (implied time scales, random walkers, committor probabilities), force field parameters, debugging
2. Nicolas Blöchliger, Ph.D.
   Primary user experience: Monte Carlo simulations of IDPs, clustering and derived data analysis techniques
   Development: Inexact progress index method, documentation
3. Davide Garolini, Ph.D.
   Primary user experience: clustering and SAPPHIRE plots
   Development: Configuration script, cross-platform support, abstraction into R ("CampaRi"), distance metrics for clustering
4. Cassiano Langini, Ph.D.
   Primary user experience: PIGS, clustering, SAPPHIRE plots, and graph-based analyses
   Development: Transition path theory
5. Nick Lyle, Ph.D.
   Primary user experience: Conformational equilibria, associativity, and thermodynamics of β-sheet formation in Q_N-peptides with and without flanking sequences
   Development: Minimizers, Wang-Landau sampling
6. Albert Mao, M.D./Ph.D.
   Primary user experience: Conformational equilibria for intrinsically disordered polypeptides with high net charge
   Development: Support for μVT and related ensembles
7. Rohit Pappu, Ph.D., full professor, see above
   User experience: Polymeric analyses of excluded volume ensembles of polypeptides
   Development: Groundwork
8. Jose Pulido
   User experience: Free energy calculations in the excluded volume limit
   Development: Thermostats
9. Adam Steffen
   User experience: Various
   Development: Exact concerted rotation and pucker sampling moves, force field porting, minimizers, documentation
10. Hoang Tran, Ph.D.
    Primary user experience: Polymeric analyses of excluded volume ensembles of polypeptides
    Development: Polymeric analyses
11. Andreas Vitalis, Ph.D., currently at the University of Zurich
    User experience: Various
    Development: Primary developer
12. Jiri Vymetal, Ph.D.
    Primary user experience: Simulations of fibril models, ABSINTH, PIGS
    Development: Distance metrics for clustering, PIGS reseeding heuristic
13. Xiaoling Wang, Ph.D.
    Primary user experience: Dimerization and conformational equilibria of Q_N-peptides
    Development: Inexact concerted rotation moves, WCA potential
14. Julian Widmer
    Primary user experience: Trajectory conversion and analysis, in particular of GROMACS-generated, explicit solvent trajectories
    Development: Tutorials, testing

Note that the above list is of the people who contributed to this release, whether in the distant part or more recently. The Pappu lab in particular has pursued and is pursuing several ongoing developments that are not part of this release, and you should redirect your requests there. The current CAMPARI development team provides support for problems, questions, bugs, scientific or parameterization errors, etc. through the dedicated SourceForge site, and we will greatly appreciate it if you make this your second stop when encountering problems (the first stop being the documentation). SourceForge is also the place to leave general feedback. Issues may occur repeatedly, and the forums may already be able to provide you with answers. If you are sure you have encountered a bug in the software, please report details of the new bug. Naturally, this should include all the information we need to be able to reproduce it.
For issues that - for whatever reason - are not fit to be presented within the SourceForge framework, you should contact the primary developers directly. This refers to requests to obtain development versions in particular.


We naturally aim to be responsive whichever way you contact us, but please understand that no member of the development team is exclusively paid to provide this type of support. Therefore, patience will be appreciated as usual.