Background Molecular dynamics has emerged as an important research methodology
covering systems to the level of millions of atoms. However, insufficient sampling often limits …

Molecular dynamics (MD) allows the study of biological and chemical systems at the
atomistic level on timescales from femtoseconds to milliseconds. It complements experiment …

S-Adenosyl-l-methionine (SAM)-responsive riboswitches play a central role in the regulation
of bacterial gene expression at the level of transcription attenuation or translation inhibition …

The severe acute respiratory syndrome (SARS) coronavirus 2 (CoV-2) variant Omicron
spread more rapid than the other variants of SARS-CoV-2 virus. Mutations on the Spike (S) …

Previous studies have shown that the method of hydrogen mass repartitioning (HMR) is a
potentially useful tool for accelerating molecular dynamics (MD) simulations. By …

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …

We present an implementation of explicit solvent all atom classical molecular dynamics (MD)
within the AMBER program package that runs entirely on CUDA-enabled GPUs. First …

A fundamental challenge in biological research is achieving an atomic-level description and
mechanistic understanding of the function of biomolecules. Techniques for biomolecular …

Mutations yield significant effect on the structural flexibility of two switch domains, SW1 and
SW2, in K-Ras, which is considered as an important target of anticancer drug design. To …

By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …