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--- z_potential_of_mean_force [2021/07/15 19:59] – created edit
+++ z_potential_of_mean_force [2021/07/15 20:05] (current) – edit
@@ Line 13: / Line 13: @@
 Step 2: Implement a stationary Colvar that holds the peptide, antibiotic, or object of interest in place while it equilibrates for a 1-4ns
-Step 5: Running simulation for official data collecting and calculating the PMF using WHAM. WHAM lookes at the deviation between the equilibrium coordinates of the spring and the spring constant to calculate the reaction coordinate.
+Step 3: Running simulation for official data collecting and calculating the PMF using WHAM. WHAM lookes at the deviation between the equilibrium coordinates of the spring and the spring constant to calculate the reaction coordinate.
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 ####It is a good idea since these will run in the debug queue to change the partition to the standard instead of the high prioritey partition. This is done by changing the dyn.scr file to say
-#!/bin/bash
+      #!/bin/bash
-sbatch -A energybio dyn.csh
+      sbatch -A energybio dyn.csh
-Step 1: Copy the files in the ___ folder into the directory. dyn_Umbrella.csh is a modified version of the dyn.csh file that implements the moving colective variable restraint. The csh file does all the work with sed and echo commands to update the position of the restraints and pass the information down a line of files.
+Step 1: Copy the files in the ____ folder into the directory. dyn_Umbrella.csh is a modified version of the dyn.csh file that implements the moving colective variable restraint. The csh file does all the work with sed and echo commands to update the position of the restraints and pass the information down a line of files.
 Before moving on be sure to recenter the trajectory so that the protein is in the center of the cell. The recenter_PMF folder is the exact same proceedure as the one used for the EDP but the references to MEMB are replaced with PROA. Run this on the last dcd file in the trajectory of data.