create_bilayer
Table of Contents
Create a Bilayer
If you want to create a lipid bilayer or lipid bilayer with protein for simulations, go to
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
- Only add neutralizing ions. This is done in Step 3 by setting the KCl concentration to zero and clicking on “Calculate Solvent Composition”
- 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)
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.txt · Last modified: 2022/05/31 16:59 by admin