Pappu Lab Software
- CAMPARI: A simulation engine that integrates several sampling methodologies including molecular dynamics, rigid body dynamics, Langevin dynamics, novel torsional molecular dynamics, and an extensive code base for Monte Carlo sampling of biological macromolecules (mainly proteins, but also supports nucleic acids). The package was developed mainly by Andreas Vitalis, building upon a coarse skeleton that was being used in the early days of the Pappu lab's existence. CAMPARI can be used for efficient calculation of free energies of solvation, neat liquids, complex fluids, and peptides in explicit solvent. However, the main advantage is its support of implicit solvent paradigms for use in Monte Carlo simulations. It is this aspect that makes CAMPARI unique. Recent work in the Pappu lab has shown that Monte Carlo simulations are particularly useful for efficient sampling of conformational space in conjunction with implicit solvation models such as ABSINTH which was also developed by Andreas Vitalis in the Pappu Lab. This model may be viewed as an efficient interpolation between the EEF1 and generalized Born (GB) paradigms. CAMPARI will also integrate support for the major variants of the GB framework to facilitate comparative calculations between different implicit solvation paradigms. We are also pursuing a collaboration with Nathan Baker's lab to develop an interface between CAMPARI and APBS to facilitate comparisons between faster solvation paradigms and the Poisson-Boltzmann framework. The CAMPARI engine, first built around the ABSINTH model, was designed for answering questions regarding conformational and binding equilibria of intrinsically disordered polypeptides. However, we anticipate a wider usage as it is tested and accepted as a bona fide engine in the biomolecular simulation community. CAMPARI will be released for use by July 01, 2009. Please stay tuned!i In the interim, we will be responsive to requests for copies of a pre-release version of the software. Interested parties should contact Rohit Pappu at pappu@wustl.edu.