Klauda Lab Simulation Wiki

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.

[[bilayer_simulations]]

==== Create a Bilayer ====

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

==== 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