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create_bilayer
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| create_bilayer [2016/11/16 15:28] – admin | create_bilayer [2022/05/31 16:59] (current) – admin | ||
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| If you want to create a lipid bilayer or lipid bilayer with protein for simulations, | If you want to create a lipid bilayer or lipid bilayer with protein for simulations, | ||
| - | http://www.charmm-gui.org/? | + | http:// |
| ==== General Rules of Thumb for Lipid Only Systems ==== | ==== General Rules of Thumb for Lipid Only Systems ==== | ||
| Line 12: | Line 12: | ||
| * Unless otherwise stated make sure the number of lipids is equal for each leaflet (total and individual) | * 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 | * The minimum number of waters per lipid should be 30 waters | ||
| - | * Do not add ions unless asked | + | * Only add neutralizing |
| * Setup a NPT system with P=1bar and T the desired temperature | * Setup a NPT system with P=1bar and T the desired temperature | ||
| + | * Select NAMD, OpenMM, and GROMACs input file generation for potential use with these programs | ||
| * Download the entire TGZ file and place this on the cluster (do not delete files as needed later) | * Download the entire TGZ file and place this on the cluster (do not delete files as needed later) | ||
create_bilayer.1479328113.txt.gz · Last modified: 2016/11/16 15:28 (external edit)