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--- rmsd [2021/09/02 11:25] – created edit
+++ rmsd [2021/09/02 11:33] (current) – edit
@@ Line 1: / Line 1: @@
-Download the script files here {{ :RMSD.tar.gz |}}
+Download the script files here {{ : RMSD.tar.gz |}}
+Use the backbone by default and change the path in the first file.
+     open unit @U read file name  "/lustre/rallsopp/glucoM4/namd/dyn"@k".dcd"
+Also update the location of the paths in the psfcrd.str by copying and pasting the .crd and .psf files into the psf folder, or adjusting the path.
+Replace the toppar folder and toppar.str file with the new ones for the new simulation.
+Adjust which analysis are used in the rmsd.scr file by removing the # in front of the #$chm lines. rmsd_all.inp is selecting all of segid PROA, and rmsd_sc.inp is selecting only the side chain.
+Run the program by typing
+sbatch rmsd.scr
+Then plot the .dat files for PROA and PROB in Matlab or another program.