Klauda Lab Simulation Wiki

If you want to create a lipid bilayer or lipid bilayer with protein for simulations, go to

http://charmm-gui.org/?doc=input/membrane.bilayer

• 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.
• 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)

• 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