README.md

NMEA-paper

Scripts used to generate data and figures for anisotropic terahertz spectroscopy paper

Romo, T. D., et al. (2020) Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis. Journal of Chemical Information and Modeling DOI: 10.1021/acs.jcim.0c00879

Simulation: parameters and input files for running the MD simulations

Spectrum: collection of scripts used to compute the VDOS and absorbance spectra, including the CHARMM input scripts

Analysis: scripts to analyze and average the data, including the projections of modes onto the difference between structures

random-projections: code to generate the distribution of dot products in high dimensions. Used to create Supplemental Figure 3.

Figures

The following describes the salient scripts used in preparation of each figure.

Figure 1

• dipolederivative_extract.py
• fastcalc.py
• postprocess.py
• process_aniso.sh

Figure 2

• dipolederivative_extract.py
• IsotropicCalcHEWL2.py
• xeig.py
• process_iso.sh
• process_vdos.sh

Figure 3

• dipolederivative_extract.py
• fastcalc.py
• postprocess.py
• process_aniso.sh

Figure 4

• dipolederivative_extract.py
• IsotropicCalcHEWL2.py
• xeig.py
• process_iso.sh
• process_vdos.sh

Figure 5

• xeig.py
• generate_diffvec.py
• process_diffvec.sh

SI Figure 1

• dipolederivative_extract.py
• IsotropicCalcHEWL2.py
• xeig.py
• process_iso.sh
• process_vdos.sh

SI Figure 2

• dipolederivative_extract.py
• IsotropicCalcHEWL2.py
• xeig.py
• process_iso.sh
• process_vdos.sh

SI Movie 1

• dipolederivative_extract.py
• fastcalc.py
• postprocess.py
• process_aniso.sh

SI Figure 3

• dipolederivative_extract.py
• fastcalc.py
• postprocess.py
• process_aniso.sh

SI Figure 4

• dipolederivative_extract.py
• fastcalc.py
• postprocess.py
• process_aniso.sh

SI Figure 5

• dipolederivative_extract.py
• fastcalc.py
• postprocess.py
• process_aniso.sh