Logs for GROMACS Simulations - Protein-ligand Complexes:

Test: Lysozyme in Water

1. Simulation Logs
2. Results

MMP9 Protein in Water

1. Simulation Logs

MMP Protein Simulations:

There are two control Molecular Dynamics simulations, that of MMP2 in SPC water, and that of Rolipram in SPC water (separately).

1. MMP2 Simulation Logs
2. Rolipram Simulation Logs
3. Results

Zebrafish Hemoglobin and Phenyl Hydrazine

New Simulations performed using singularity image with the conda-forge version of GROMACS (version 2024.2) compiled for nVidia-GPUs, as well as gromacs_py and mdanalysis.

See README for zeb_hb

Docs

1. MD-Tutorials by Justin A. Lemkul- Living J. Comp. Mol. Sci. 1 (1): 5068 (2018).
2. GROMACS on CompChems
3. GROMACS Website
4. DNA-ligand simulation in gromacs-py
5. ACPYPE-AnteChamber PYthon Parser interfacE
6. RMSF Analysis of MD Simulation
7. How to calculate RMSD of complex - researchgate
8. GROMACS-Protein-Ligand
9. GROMACS: MD Simulation of a Protein-Ligand Complex
10. Gromacs Protein Ligand Complex Simulations
11. Protein-Ligand Interactions
12. How to Compare Proteins - Physics 17, 40 (2024).
13. CHARMM GUI
14. SwissParams CHARMM topology generator
15. Hydrogen Bond Tutorial
16. Bioinformatics Stackexchange discussion on Hydrogen adding to PDB
17. Automated Topology Builder