SKM 2023 – wissenschaftliches Programm

Bereiche | Tage | Auswahl | Suche | Aktualisierungen | Downloads | Hilfe

BP: Fachverband Biologische Physik

BP 11: Poster Session I

BP 11.17: Poster

Dienstag, 28. März 2023, 12:30–15:30, P1

Neighbor list artifacts in molecular dynamics simulations — •Hyuntae Kim — Max Planck Institute for Biophysics — International Max Planck Research School on Cellular Biophysics

Molecular dynamics simulations are widely used in biophysics. To aid non-expert users, most simulation packages provide default values for key input parameters. We found that the default setting of the neighbor list cut-off rlist in the GROMACS package is not sufficient to prevent various artifacts in certain systems. Beyond an already known significant energy drift, we observed catastrophic box deformations of large membrane systems with a semi-isotropically coupled Parrinello Rahman (PR) barostat, rapid oscillations in the pressure, and asymmetric deformations of the box shape. We traced the cause of these artifacts to infrequent neighbor-list updates resulting in missed long-range Lennard-Jones interactions that are systematically attractive. We find that for the small molecular systems commonly simulated, these effects tend to be masked. We present measures to diagnose the problem and guidelines for practitioners.