Matches in SemOpenAlex for { <https://semopenalex.org/work/W4384661807> ?p ?o ?g. }
Showing items 1 to 67 of
67
with 100 items per page.
- W4384661807 abstract "Molecular dynamics (MD) simulations are widely used in biophysical research. To aid non-expert 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 result in missed long-range attractive Lennard-Jones 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 confirmed that similar effects are present in MD simulations of neat water in atomistic and coarse-grained representations. Whereas the slight pressure imbalances likely have minimal impact in most current MD simulations, we expect their impact to grow in studies of ever-larger systems, in particular in combination with anisotropic pressure coupling. We present measures to diagnose problems with missed interactions and guidelines for practitioners to avoid them, including estimates for appropriate values for the outer cutoff r_l and the number of time steps nstlist between neighbor list updates." @default.
- W4384661807 created "2023-07-20" @default.
- W4384661807 creator A5025294516 @default.
- W4384661807 creator A5061316402 @default.
- W4384661807 creator A5089799904 @default.
- W4384661807 date "2023-07-18" @default.
- W4384661807 modified "2023-09-26" @default.
- W4384661807 title "Neighbor List Artifacts in Molecular Dynamics Simulations" @default.
- W4384661807 doi "https://doi.org/10.26434/chemrxiv-2023-zbj6j" @default.
- W4384661807 hasPublicationYear "2023" @default.
- W4384661807 type Work @default.
- W4384661807 citedByCount "0" @default.
- W4384661807 crossrefType "posted-content" @default.
- W4384661807 hasAuthorship W4384661807A5025294516 @default.
- W4384661807 hasAuthorship W4384661807A5061316402 @default.
- W4384661807 hasAuthorship W4384661807A5089799904 @default.
- W4384661807 hasBestOaLocation W43846618071 @default.
- W4384661807 hasConcept C121332964 @default.
- W4384661807 hasConcept C121864883 @default.
- W4384661807 hasConcept C127413603 @default.
- W4384661807 hasConcept C131584629 @default.
- W4384661807 hasConcept C155281189 @default.
- W4384661807 hasConcept C159985019 @default.
- W4384661807 hasConcept C188198153 @default.
- W4384661807 hasConcept C191897082 @default.
- W4384661807 hasConcept C192562407 @default.
- W4384661807 hasConcept C202444582 @default.
- W4384661807 hasConcept C204323151 @default.
- W4384661807 hasConcept C2778217198 @default.
- W4384661807 hasConcept C33923547 @default.
- W4384661807 hasConcept C41008148 @default.
- W4384661807 hasConcept C59593255 @default.
- W4384661807 hasConcept C62520636 @default.
- W4384661807 hasConcept C78519656 @default.
- W4384661807 hasConceptScore W4384661807C121332964 @default.
- W4384661807 hasConceptScore W4384661807C121864883 @default.
- W4384661807 hasConceptScore W4384661807C127413603 @default.
- W4384661807 hasConceptScore W4384661807C131584629 @default.
- W4384661807 hasConceptScore W4384661807C155281189 @default.
- W4384661807 hasConceptScore W4384661807C159985019 @default.
- W4384661807 hasConceptScore W4384661807C188198153 @default.
- W4384661807 hasConceptScore W4384661807C191897082 @default.
- W4384661807 hasConceptScore W4384661807C192562407 @default.
- W4384661807 hasConceptScore W4384661807C202444582 @default.
- W4384661807 hasConceptScore W4384661807C204323151 @default.
- W4384661807 hasConceptScore W4384661807C2778217198 @default.
- W4384661807 hasConceptScore W4384661807C33923547 @default.
- W4384661807 hasConceptScore W4384661807C41008148 @default.
- W4384661807 hasConceptScore W4384661807C59593255 @default.
- W4384661807 hasConceptScore W4384661807C62520636 @default.
- W4384661807 hasConceptScore W4384661807C78519656 @default.
- W4384661807 hasLocation W43846618071 @default.
- W4384661807 hasOpenAccess W4384661807 @default.
- W4384661807 hasPrimaryLocation W43846618071 @default.
- W4384661807 hasRelatedWork W1521427385 @default.
- W4384661807 hasRelatedWork W1984889076 @default.
- W4384661807 hasRelatedWork W1986891341 @default.
- W4384661807 hasRelatedWork W1997673248 @default.
- W4384661807 hasRelatedWork W2027596801 @default.
- W4384661807 hasRelatedWork W2059613462 @default.
- W4384661807 hasRelatedWork W2071566964 @default.
- W4384661807 hasRelatedWork W2376369230 @default.
- W4384661807 hasRelatedWork W3045719294 @default.
- W4384661807 hasRelatedWork W2190552620 @default.
- W4384661807 isParatext "false" @default.
- W4384661807 isRetracted "false" @default.
- W4384661807 workType "article" @default.