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create_bilayer
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If you want to create a lipid bilayer or lipid bilayer with protein for simulations, go to
http://www.charmm-gui.org/?doc=input/membrane
General Rules of Thumb for Lipid Only Systems
- Build bilayers based on number of lipids not size
- Unless otherwise stated make sure the number of lipids is equal for each leaflet (total and individual)
- The minimum number of waters per lipid should be 30 waters
- Do not add ions unless asked
- Setup a NPT system with P=1bar and T the desired temperature
- Download the entire TGZ file and place this on the cluster (do not delete files as needed later)
General Rules of Thumb for Lipid+Protein Systems
- Choose a bilayer composition under the direction of a senior student, postdoc or Dr. Klauda
- Be careful with transmembrane proteins and placement using OPM
- If doing peptides with HMMM, be sure to consult with Dr. Klauda
create_bilayer.1479327695.txt.gz · Last modified: 2016/11/16 15:21 (external edit)