Trajectory Convergence Analysis

run_rmsd_analysis

run_rmsd_analysis identifies converged trajectory segments by comparing RMSD means and standard deviations for ligand, protein, and active site residues (5 Angstrom default). The same analysis runs automatically as part of run_md step 4 from Running Molecular Dynamics.

Usage

run_rmsd_analysis -h

usage: run_rmsd_analysis [-h] [-i FILENAME [FILENAME ...]] [--rmsd_type backbone [backbone ...]] [--time_ranges 0-1 5-10 9-10 [0-1 5-10 9-10 ...]] [-d dirname]
                       [--paint_by PAINT_BY] [-o OUT_SUFFIX] [--title RMSD Mean vs RMSD Std]

Run rmsd analysis for StreaMD output files

options:
  -h, --help            show this help message and exit
  -i FILENAME [FILENAME ...], --input FILENAME [FILENAME ...]
                        input file(s) with rmsd. Supported formats: *.csv. Required columns: time(ns) ligand_name system. Sep: /\t.
  --rmsd_type backbone [backbone ligand ActiveSite]
                        Column names in the input file to use for the analysis 
  --time_ranges 0-1 5-10 9-10 [0-1 5-10 9-10 ...]
                        Time ranges in nanoseconds. Default: Default: start-end, middle-end, end-1 (in nanoseconds)
  -d dirname, --wdir dirname
                        Output files directory
  --paint_by csv_file   File to paint by additional column. Required columns: - Protein-ligand simulations: system\tligand_name. - Protein only in water simulations: system. Sep: /\t. The plot will be painted by any other than system and
                        ligand_name column.
  -o OUT_SUFFIX, --out_suffix OUT_SUFFIX
                        Suffix for output files
  --title RMSD Mean vs RMSD Std
                        Title for html plot. Default: RMSD Mean vs RMSD Std

Examples

Preferred (uses run_md analysis step):

run_md --wdir_to_continue md_files/md_run/protein_H_HIS_ligand_1 md_files/md_run/protein_H_HIS_ligand_2 --steps 4 -d md_files

Direct usage:

run_rmsd_analysis -i rmsd_all_systems.csv --rmsd_type "backbone" "ligand" "ActiveSite5.0A" \
  --paint_by exp_data.csv -o protein --title "Protein. RMSD Mean vs RMSD Std" --time_ranges 0-1 0-2 0-10 5-10 9-10

Outputs

rmsd_mean_std_time-ranges_*start-time*.csv - output data
rmsd_mean_std_time-ranges_*start-time*.html - interactive visualization

See Outputs and Files for where RMSD analysis artifacts are stored within each run.