Neighbor List Artifacts in Molecular Dynamics Simulations

Area of Science:

• Biophysical research
• Computational chemistry
• Molecular modeling

Background:

• Molecular dynamics (MD) simulations are crucial in biophysics.
• Default parameters in simulation packages like GROMACS are often used by nonexperts.
• Previous studies have not fully addressed potential issues with default MD parameters.

Purpose of the Study:

• To identify the cause of unphysical membrane deformation in GROMACS MD simulations using default parameters.
• To investigate the impact of parameter choices on pressure tensor accuracy.
• To provide guidelines for optimizing MD simulation parameters for accurate results.

Main Methods:

• Performed MD simulations using the GROMACS package with default settings.
• Analyzed membrane deformation and pressure tensor components.
• Investigated the role of outer cutoff (r_l) and neighbor list update frequency (nstlist).
• Tested simulations with neat water in both atomistic and coarse-grained models.

Main Results:

• Default GROMACS parameters led to membrane crumpling due to missed nonbonded interactions from short cutoffs and infrequent updates.
• Systematic pressure imbalances caused asymmetric box deformations.
• Dual pair lists with dynamic pruning resulted in pressure oscillations.
• Similar issues were observed in simulations of water.

Conclusions:

• Default MD parameters, particularly short outer cutoffs and infrequent neighbor list updates, can introduce significant artifacts in simulations of large systems like membranes.
• These artifacts, though minor in smaller systems, can become critical in coarse-grained simulations of large-scale biological systems.
• Recommendations are provided for diagnosing and avoiding these issues by optimizing r_l and nstlist parameters.