Can anyone help give me detailed steps as how I can add parameters in gromacs such as force field parameters, what to edit in pdb file and wat are the other steps in detail. I docked homocysteine c ...

MD simulation data is colored by run as indicated. Non-glycosylated MD simulation data is shown on the left, glycosylated MD simulation data is shown on the right. The conformational space explored in ...

Water is the most prevalent component of biomolecular simulations—from protein ensembles to nucleic acids—and inaccurately simulating it can lead to errors for research results in biomolecular ...

In this study, the atomic level interactions between wild type and G1202R mutant of ALK protein with potential inhibitors have been analysed from MD simulation trajectories in order to identify a ...

The reactive force field (ReaxFF) molecular dynamics (MD) simulations were performed to mimic the two-phase equilibrium between silica melts and bulk water at conditions of 1473 K and 100–700 MPa. The ...

The success of a molecular dynamics simulation depends on the accuracy of the force field used to define the atomic interactions. It is challenging to train both classical and modern machine-learning ...

In this study, we demonstrate that employing ECC approximated polarization in molecular dynamics simulations allows for the prediction of multiple channel properties: conductance, ion occupancy, ...

Molecular dynamics (MD) simulations have become an increasingly indispensable tool for investigating the atomic-scale mechanisms of the cold spray deposition process. Currently, copper (Cu) is ...

To-scale snapshots from molecular dynamics simulations illustrating hot-spot formation during pore collapse. The images show pores with diameters of 60, 100, 200 and 300 nanometers, illustrating ...

One of the notable advantages of idpGAN is its ability to circumvent the kinetic barriers that constrain MD simulations. Because generative models directly learn the equilibrium distribution of ...

Molecular dynamics simulations reveal that lipid binding at antibody loops and framework regions stabilizes membrane interactions, providing molecular details for neutralization mechanisms and ...