RMSD plots can be used to determine how long it takes for the system to stabilize. The RMSD should plateau at some point during the neutral dynamics, at a value between 1-2A. The time between the start of dynamics and the plateau is how much of the trajectory should be excluded from future analysis. Our current protocol is to use the average structure over the length of the entire trajectory as the reference for the RMSD calculation.
Work Flow
Step 1
The first step is to strip the experimental trajectories so an average structure can be made. Run /mindstore/home33ext/kscopino/BIN/make_cpptraj_1a_strip.py to create the cpptraj input files for each run (cpptraj_1a_strip.in) and the shell script to submit cpptraj jobs to the scheduler (run_cpptraj_1a_strip.sh). Then submit run_cpptraj_1a_strip.sh. The output will be mdcrd_nd_x_strip in the same directory as the unstripped trajectory.
Step 2
The second step is to create the average structure of each stripped trajectory. Run /mindstore/home33ext/kscopino/BIN/make_cpptraj_1b_avgstruct.py to create the cpptraj input files for each run (cpptraj_1b_avgstruct.in) and the shell script to submit cpptraj jobs to the scheduler (run_cpptraj_1b_avgstruct.sh). Then submit run_cpptraj_1b_avgstruct.sh. The output will be avg_struct.rst in the DATA directory.
Step 3
The third step is to perform the RMSD calculation. Run /mindstore/home33ext/kscopino/BIN/make_cpptraj_1c_rms.py to create the cpptraj input files for each run (cpptraj_1c_rms.in) and the shell script to submit cpptraj jobs to the scheduler (run_cpptraj_1c_rms.sh). Then submit run_cpptraj_1c_rms.sh. The output will be three files, rmsd_x_local_bkbone.dat, rmsd_x_NOTrestr_bkbone.dat and rmsd_x_restr_bkbone.dat that look at the RMSD of the 12-residue local area (A-site codon, +1 codon, tRNA anticodon, CAR), of free residues, and of onion shell residues, respectively. All three use only backbone atoms in the calculation.
Step 4
The RMSD is calculated for every frame that is written into the trajectory. When plotted, this becomes quite noisy. Run the binning script /mindstore/home33ext/kscopino/BIN/make_cpptraj_1d_bin.py to take the average of each nanosecond for graphing. The output can be visually inspected in the terminal, or directed into a file for easily plotting in Excel (python make_cpptraj_1d_bin.py > output.txt).
