A polymer chain of N atoms enjoys 3N-6 internal degrees of freedom, which gives rise to
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …

The free energy landscape concept that describes enzymes as an ensemble of differently
populated conformational sub-states in dynamic equilibrium is key for evaluating enzyme …

We identify hardware that is optimal to produce molecular dynamics (MD) trajectories on
Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we …

Proper treatment of nonbonded interactions is essential for the accuracy of molecular
dynamics (MD) simulations, especially in studies of lipid mono-and bilayers. The use of the …

We assess costs and efficiency of state-of-the-art high-performance cloud computing and
compare the results to traditional on-premises compute clusters. Our use case is atomistic …

Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important
role in many biological phenomena, roles that range from stabilization of biomolecular …

Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-
acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid …

We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular
dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) …

The graphics processing unit (GPU) has become an integral part of today's mainstream
computing systems. Over the past six years, there has been a marked increase in the …

As access to computational resources continues to increase, free-energy calculations have
emerged as a powerful tool that can play a predictive role in a wide range of research areas …