Simulations of OMPC, SOPC, and DOPC bilayers and monolayers at three different sizes. CHARMM36 with OPC water model
Authors/Creators
- 1. Institute of Biotechnology, University of Helsinki
Description
Simulations of OMPC, SOPC, and DOPC bilayers and monolayers with the CHARMM36 force field and OPC water. 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"), separated into two tar archives, one for bilayers and one for monolayers.
- 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, and are not included in the tar arcives.
- 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 CHARMM36 force field is obtained from http://mackerell.umaryland.edu/charmm_ff.shtml
Files
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Additional details
Funding
- Research Council of Finland
- A Molecular View on the Health Hazards of Ultrafine Particulate Matter 338160