Executive Summary : | Free energy calculations using alchemical free energy perturbation and thermodynamic integration methods are widely used in predicting binding free energies of drug molecules, solvation free energies of molecules and ions, protein aggregation affinities, pKa calculations etc. and have wide spread applications in drug development, understanding important biochemical processes and chemical reactions, and several industrially relevant problems. Usually, such free energy calculations are performed using molecular dynamics. However, these conventional free energy methods have several limitations when used for studying complex soft-matter systems. This pertains to the poor sampling of the conformational space. This often results in erroneous free energy estimates, poor convergence and hysteresis. We are proposing here a new method (Lambda-TASS) which can overcome this problem by ensuring rigorous conformational sampling. This will be achieved by carrying out free energy perturbation/thermodynamic integration using the framework of Temperature Accelerated Sliced Sampling (TASS) enhance sampling approach. The Lambda-TASS method is designed here in such a manner that large number of collective variables can be chosen for rigorous conformational sampling, while a controlled sampling of the alchemical order parameter is performed. The method will provide flexibility in choosing different transverse coordinates for different values of the alchemical order parameters. In these aspects, the method is likely to outperform the conventional and state-of-the-art free energy methods. The method will be implemented in GROMACS, which is an open-source and popular software for molecular simulations. The new method will be then benchmarked in detail. We will applying Lambda-TASS in various problems related to our ongoing efforts in understanding antibiotic resistance by bacteria at the molecular level and in developing new inhibitors against beta-lactamase enzymes that are mainly responsible for widespread antibiotic resistance. Finally, we plan to further extend the method for pKa calculations in beta-lactamase enzymes. |