Simulations of POPC bilayers and monolayers at three different sizes. CHARMM36 with OPC, TIP3P, and TIPS3P water models with modified masses

dc.contributor.affiliationInstitute of Biotechnology, University of Helsinki-Javanainen, Matti
dc.contributor.authorJavanainen, Matti
dc.contributor.roleJavanainen, Matti Researcher
dc.date.accessioned2025-04-29T14:02:38Z
dc.date.issued2024
dc.date.issued2024
dc.descriptionSimulations of POPC bilayers and monolayers with the CHARMM36 force field and mass-scaled standard TIP3P, CHARMM-specific TIP3P ("TIPS3P"), and OPC water models. These water models have approximately equal viscosities. Three system sizes are used: small ("S", 64 lipids), medium ("M", 256 lipids), and large ("L", 1024 lipids). All simulations are 1 µs long. The simulations are performed using GROMACS, and for each system the following are provided for bilayers ("BIL") and monolayers ("MONO"): run input file (tpr) energy file (edr) trajectory file (xtc) checkpoint file (cpt)  final structure (gro) Additionally, the following are shared by the monolayer and bilayer: index file (ndx) topology file (top) The simulation parameter files (mdp) are provided separately for bilayers and monolayers. The molecular topologies (top) are included in TOP.tar. The TIPS3P data are available in version 2. The CHARMM36 force field is obtained from http://mackerell.umaryland.edu/charmm_ff.shtml
dc.identifierhttps://doi.org/10.5281/zenodo.13346571
dc.identifier.urihttps://datakatalogi.helsinki.fi/handle/123456789/5261
dc.rights.licensecc-by-4.0
dc.titleSimulations of POPC bilayers and monolayers at three different sizes. CHARMM36 with OPC, TIP3P, and TIPS3P water models with modified masses
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