690 citations · 2.3k across the 20 of their papers we have counts for
22 papers
Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond
Kenichiro Takaba, Iván Pulido, Pavan Kumar Behara +11
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is in…
Towards Molecular Simulations that are Transparent, Reproducible, Usable By Others, and Extensible (TRUE)
Matthew W. Thompson, Justin B. Gilmer, Ray A. Matsumoto +6
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations…
Formalizing Atom-typing and the Dissemination of Force Fields with Foyer
Christoph Klein, Andrew Z. Summers, Matthew W. Thompson +5
A key component to enhancing reproducibility in the molecular simulation community is reducing ambiguity in the parameterization of molecular models. Ambiguity in molecular models…
The Influence of Ceramide Tail Length on the Structure of Bilayers Composed of Stratum Corneum Lipids
T. C. Moore, R. Hartkamp, C. R. Iacovella +2
Lipid bilayers composed of non-alpha hydroxy sphingosine ceramide (CER NS), cholesterol (CHOL), and free fatty acids (FFA), which are components of the human skin barrier, are stud…
Development of a coarse-grained water forcefield via multistate iterative Boltzmann inversion
Timothy C. Moore, Christopher R. Iacovella, Clare McCabe
A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the k-means algorithm is used to dynamically map multiple water m…
Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion
Timothy C. Moore, Christopher R. Iacovella, Clare McCabe
In this work, an extension to the standard iterative Boltzmann inversion (IBI) method to derive coarse-grained potentials is proposed. It is shown that the inclusion of target data…