This page is dedicated to the research concerning coarse-grained molecule modelling. The current activity is directed towards promotion and further development of RE2 coarse-grained interaction potential, introducted by R. Everaers and R. Ejtehadi (see Publications) as an improvement of the well-known Gay-Berne potential. Having an identical parameter space, the RE-squared potential agrees significantly better with the exact atomic summations, has no unphysical large-distant limit and avoids the introduction of empirical adjustable parameters.
You will find the pre-prints of the related publications and group members in the corresponding sections. Furthermore, the automatic parameterization tool for arbitrary molecules and software development libraries are available in the Downloads section.
A free, general purpose molecular dynamics software based on RE-squared interactions is under rapid development at the moment and test releases will be available soon. Feel free to contact us for comments and questions.
- M. Babadi, R. Everaers, M.R. Ejtehadi, Coarse-grained Interaction Potentials for Anisotropic Molecules, to appear in J. Chem. Phys.
- M. Babadi, R. Everaers, M. R. Ejtehadi, Analytical First Derivatives of RE-squared Interaction Potential, to be Submitted to J. Comp. Phys.
- R. Everaers, M.R. Ejtehadi Interaction potentials for soft and hard ellipsoids, Phys. Rev. E 67, 041710 (2003)
You can download the software tools for parametrization and implementation of the RE-squared interaction potential in this section. You are free to re-distribute and modify the provided codes for non-commercial purposes by giving appropriate credits to the authors. The details of the terms of usage have been provided with the software packages. Please note that these codes are still in the under development, are not fully documented yet and are subject to substantial changes. Should you have any questions, feel free to contact us.
- Automatic Parametrization Code (pre-release) (The MATLAB (and GNU/Octave) code for automatic parametrization of homo/heterogeneous RE-squared interactions between arbitrary molecules using MM3 atomic force-field. Please read the attached Readme file for instructions)
- C++ Library (pre-release) (C++ routines for evaluation of RE-squared potential, implementing analytic derivatives. This code portion depends on GSL linear algebra routines. Please read the attached Readme file for compiling and linking instructions)