Universal QM/MM approaches for general nanoscale applications
Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address
chemical phenomena in complex molecular environments. Whereas this modeling approach …
chemical phenomena in complex molecular environments. Whereas this modeling approach …
Markov state models provide insights into dynamic modulation of protein function
Conspectus Protein function is inextricably linked to protein dynamics. As we move from a
static structural picture to a dynamic ensemble view of protein structure and function, novel …
static structural picture to a dynamic ensemble view of protein structure and function, novel …
Learning local equivariant representations for large-scale atomistic dynamics
A simultaneously accurate and computationally efficient parametrization of the potential
energy surface of molecules and materials is a long-standing goal in the natural sciences …
energy surface of molecules and materials is a long-standing goal in the natural sciences …
Development and benchmarking of open force field 2.0. 0: the Sage small molecule force field
We introduce the Open Force Field (OpenFF) 2.0. 0 small molecule force field for drug-like
molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF …
molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF …
Linear atomic cluster expansion force fields for organic molecules: beyond rmse
We demonstrate that fast and accurate linear force fields can be built for molecules using the
atomic cluster expansion (ACE) framework. The ACE models parametrize the potential …
atomic cluster expansion (ACE) framework. The ACE models parametrize the potential …
Balanced protein–water interactions improve properties of disordered proteins and non-specific protein association
Some frequently encountered deficiencies in all-atom molecular simulations, such as
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
Building force fields: An automatic, systematic, and reproducible approach
The development of accurate molecular mechanics force fields is a significant challenge that
must be addressed for the continued success of molecular simulation. We developed the …
must be addressed for the continued success of molecular simulation. We developed the …
Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)
M Schauperl, PS Nerenberg, H Jang… - Communications …, 2020 - nature.com
The restrained electrostatic potential (RESP) approach is a highly regarded and widely used
method of assigning partial charges to molecules for simulations. RESP uses a quantum …
method of assigning partial charges to molecules for simulations. RESP uses a quantum …
Building a more predictive protein force field: a systematic and reproducible route to AMBER-FB15
The increasing availability of high-quality experimental data and first-principles calculations
creates opportunities for developing more accurate empirical force fields for simulation of …
creates opportunities for developing more accurate empirical force fields for simulation of …
Escaping atom types in force fields using direct chemical perception
Traditional approaches to specifying a molecular mechanics force field encode all the
information needed to assign force field parameters to a given molecule into a discrete set of …
information needed to assign force field parameters to a given molecule into a discrete set of …