Differences

This shows you the differences between two versions of the page.

--- create_bilayer [2016/11/16 15:13] – admin
+++ create_bilayer [2022/05/31 16:59] (current) – admin
@@ Line 1: / Line 1: @@
 [[bilayer_simulations]]
+==== Create a Bilayer ====
 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
+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