figshare
Browse
si2-poster-april2018.pdf (1.63 MB)

NSF-SI2-2018-poster: Enhanced software tools for biomolecular free energy calculations

Download (1.63 MB)
poster
posted on 2018-04-20, 15:11 authored by Christopher RolandChristopher Roland, Celeste Sagui
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.

Funding

NSF 1534941

History

Usage metrics

    Licence

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC