Calculate RMSD and RMSF

Hello @passive-radio

I created description webpage that show how to calculate RMSD and RMSF.

https://flat35hd99.github.io/md_stepbystep/analyse/rmsd_and_rmsf.html

Could you check this page and perform at your calculation ? Actually, this template calculate RMSD and RMSF automatically but the initial configuration is not correct. See 3sampling/input/cpptraj. It calculate RMSD and RMSF but the number of residues is not correct. Please change the residue number from 1-36 to 1-N that N is the number of total residues`

After rewrite, save this file as 3sampling/run_cpptraj.sh. Change $PREFIX.

#!/bin/sh -eu

prefix=$PREFIX

module purge
source $prefix/util/load_amber_on_cloud

for run in `seq 0 4`;do
  output=$prefix/3sampling/output/0${run}

  for step in pre_sampling_0 pre_sampling_1 sampling;do
    cd $output/$step
    cpptraj -i $prefix/3sampling/input/cpptraj
  done
done

After save,

ssh fc # Connect flow-cloud. Run this command at your local machine
cd /path/to/3sampling
chmod +x run_cpptraj.sh # Add executable permissions
source ../util/load_amber_on_cloud
./run_cpptraj.sh

After a few minutes, you will get correct RMSD and RMSF. You are highly recommended to plot the data using some software you like. VScode can run jupyter notebook at remote machine. It is convenient to check the data interactively.

flat35hd99 / md_template

Calculate RMSD and RMSF #3