I came across a manuscript under review titled “Neighbor List Artifacts in Molecular Dynamics Simulations”. see "Neighbor List Artifacts in Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage" This study claimed that many non-expert users rely on default values for key inputs, which can lead to deformation in some cases, such as large membranes simulations. The study also suggested that most simulations suffer from inappropriate parameters for outer cutoff, ri and nstlist, resulting in missing long-range Lennard-Jones interactions. I would appreciate any comments and suggestions.
I don't know about 'most simulations' suffering from it, but the issue is real. See for example: https://doi.org/10.1016/j.bbamem.2016.02.004.
Dear Kanski
Would you please explain about parameters setting in your simulations? for example rc and r in a protein-ligand simulation?
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