Neighbor List Artifacts in Molecular Dynamics Simulations.

ABSTRACT: Molecular dynamics (MD) simulations are widely used in biophysical research. To aid nonexpert users, most simulation packages provide default values for key input parameters. In MD simulations using the GROMACS package with default parameters, we found large membranes to deform under the action of a semi-isotropically coupled barostat. As the primary cause, we identified overly short outer cutoffs and infrequent neighbor list updates that resulted in missed nonbonded interactions. Small but systematic imbalances in the apparent pressure tensor then induce unphysical asymmetric box deformations that crumple the membrane. We also observed rapid oscillations in averages of the instantaneous pressure tensor components and traced these to the use of a dual pair list with dynamic pruning. We con

SUBMITTER: Kim H 

PROVIDER: S-EPMC10720336 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature