NSF-SI2-2018-poster: Enhanced software tools for biomolecular free energy calculations
2018-04-20T15:11:32Z (GMT) by
The single-most important quantity for describing biomolecular and chemical systems at equilibrium is the free energy. Unfortunately, calculating free energies is notoriously difficult and computationally expensive. The problem is particularly pressing for many biomolecular systems which are characterized by complicated free energy landscapes that are hard to explore with regular molecular dynamics simulations. We have developed a set of software tools centered around our Adaptively Biased Molecular Dynamics (ABMD) method with multiple walker and replica exchange molecular dynamics (REMD) extensions. ABMD is an umbrella sampling method with a time-dependent biasing potential for calculate free energy landscapes and configurational sampling. The software suite, along with Steered Molecular Dynamics (SMD) method has been released as part of the AMBER software package. Our proposal aims at taking this set of software tools to the next level by making the suite PMEMD compatable and adding new algorithms that enhancing the capabilities of the ABMD method.