Assessing the Current State of Amber Force Field Modifications for DNA
University of Utah · University of Montana · +4 more institutions
Abstract
The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling,…
Citation impact
- FWCI
- 16.19
- Percentile
- 100%
- References
- 83
Authors
7- RGRodrigo Galindo‐MurilloCorresponding
University of Utah, University of Montana
- JRJ.C. Robertson
University of Utah, University of Montana
- MZMarie Zgarbová
Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc
- JŠJiřı́ Šponer
Czech Academy of Sciences, Czech Academy of Sciences, Institute of Biophysics, Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc
- MOMichal Otyepka
Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc
Topics & keywords
- Force field (fiction)
- Molecular dynamics
- Computer science
- Sampling (signal processing)
- Field (mathematics)
- Computational science
- Statistical physics
- Chemistry
- Clean water and sanitation