rmsd
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.
rmsd.txt · Last modified: 2021/09/02 11:33 by edit