Long-time-step molecular dynamics can retard simulation of protein-ligand recognition process.

ABSTRACT: Molecular dynamics (MD) simulation of biologically relevant processes at realistic time scale and atomistic precision is generally limited by prohibitively large computational cost, due to its restriction of using an ultrashort integration time step (1-2 fs). A popular numerical recipe to reduce the associated computational burden is adopting schemes that would allow relatively longer-time-step for MD propagation. Here, we explore the perceived potential of one of the most frequently used long-time-step protocols, namely the hydrogen mass repartitioning (HMR) approach, in alleviating the computational overhead associated with simulation of the kinetic process of protein-ligand recognition events. By repartitioning the mass of heavier atoms to their linked hydrogen atoms, HMR leverages arou

SUBMITTER: Sahil M 

PROVIDER: S-EPMC10027446 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature