Benchmarking Adaptive Steered Molecular Dynamics (ASMD) on CHARMM Force Fields
Chemistry Europe: European Chemical Societies Publishing
BSKB’s Hailey Bureau, Ph.D., co-authored a research article entitled “Benchmarking Adaptive Steered Molecular Dynamics (ASMD) on CHARMM Force Fields”. Although prepared during her time in graduate school, the paper has now been published on May 20, 2022 in ChemPhysChem here.
The article focuses on “The potentials of mean force (PMFs) along the end-to-end distance of two different helical peptides have been obtained and benchmarked using the adaptive steered molecular dynamics (ASMD) method. The results depend strongly on the choice of force field driving the underlying all-atom molecular dynamics, and are reported with respect to the three most popular CHARMM force field versions: c22, c27 and c36. Two small peptides, ALA 10 and 1PEF, serve as the particular case studies. The comparisons between the versions of the CHARMM force fields provides both a qualitative and quantitative look at their performance in forced un- folding simulations in which peptides undergo large changes in structural conformations. We find that ASMD with the underlying c36 force field provides the most robust results for the selected benchmark peptides.”