MD Analysis - Molecular Dynamics Simulation

This tutorial provides standardized guidance for analyzing molecular dynamics simulations performed with GROMACS and GetContacts. It covers RMSD, RMSF, and residue-ligand contact frequency analyses.

>>Click to download analysis scripts<<

I. RMSD Analysis (rmsd.py)

Overview: RMSD measures the overall structural deviation of the system over time relative to a reference conformation.

Prerequisites:

• pbc.xtc - Trajectory file with periodic boundary conditions treated
• md.tpr - Topology/run input file for RMSD calculation

GROMACS Command:

gmx rms -f pbc.xtc -s md.tpr -o rmsd_protein.xvg

Outputs:

• rmsd_summary.txt - Statistical summary of RMSD
• rmsd_timeseries.tsv - Time-series RMSD values

II. RMSF Analysis (rmsf.py)

Overview: RMSF measures the fluctuation amplitude of each residue over time, identifying flexible regions.

GROMACS Command:

gmx rmsf -f pbc.xtc -s md.tpr -o rmsf_protein.xvg -oq bfac.pdb -res

Outputs:

• rmsf_profile.tsv - RMSF value for each residue
• rmsf_summary.txt - Statistical summary of RMSF

III. Residue Contact Frequency Analysis (frequency.py)

Overview: Computes residue-ligand contact frequencies using GetContacts to identify key binding residues.

GetContacts Command:

get_dynamic_contacts.py --topology md.gro --trajectory pbc.xtc --output loop-ligand_all.tsv --cores 10 --sele "protein" --sele2 "resname LIG" --itypes all

Outputs:

• residue_ligand_contacts.tsv - Detailed residue-ligand contact table

General Notes

• Ensure input files are correctly formatted and paths are properly set in Python scripts
• Check script configurations for proper file paths and output directories

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