Molecular dynamics articles from across Nature Portfolio

Electronic spin influences chemistry profoundly, but its role in surface chemistry is poorly established. Now the spin-dependent reaction probabilities of oxygen atoms with a graphite surface have been studied. Molecular dynamics simulations help elucidate the mechanism for spin-flipping, which is observed to occur with low probability in surface scattering experiments.

Relative binding free energy calculations are widely used to guide drug discovery by accurately computing binding affinity, however, these simulations remain complicated to set up, computationally expensive to run, and technically challenging to scale up. Here, the authors develop an end-to-end relative free energy workflow based on a non-equilibrium switching approach that calculates the binding free energies starting from SMILES strings.

The hydrophobic gating is believed to function in various ion channels. Here, the authors use MD simulations to assess how dewetting of the channel pore modulates the function and conformational transition of the potassium channels.

Hydrophilic metal-organic framework NU-1500-Cr is a high performing water harvesting material, but the mechanism through which it adsorbs water remains unclear. Here, molecular dynamics simulations and infrared spectroscopy are used to follow the water adsorption process in NU-1500-Cr from the initial hydration stage to complete filling of the MOF pores.

Here the authors report SBCG2 an update to the neural network based, Shape-Based Coarse Graining (SBCG) approach for creating coarse grained molecular topologies with atomistic detail. They show how SBCG2 can reduce the computational costs of simulating very large assemblies like the HIV-1 capsid allowing simulation on commodity hardware.

Direct spectroscopic probes of the impact of structure on dynamical processes in liquids remain scarce. Here, the authors use molecular dynamics simulations to show that the correlation between vibrational coupling and the local tetrahedral structure of liquid water can be studied via hybrid terahertz- and infrared-Raman spectroscopy.