I want to understand the basic concept of molecular dynamics simulation and how to interpret the results. I used GROMACS for running a ligand-protein complex simulation now want to interpret those results for my publication.
http://www.mdtutorials.com/gmx/
https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0
Code GROMACS Normal Mode Analysis Script
Code GROMACS MD Analysis Script
Code GROMACS (AMBER)
Code GROMACS (CHARMM)
And then you can start and learn by yourself.
HTH!
Kindly refer to the following sources for understanding basics of MD simulation and your queries regarding analyzing MD simulation results.
Papers:
Molecular dynamics simulations of biomolecules (https://www.nature.com/articles/nsb0902-646)
Article Molecular Dynamics: Survey of Methods for Simulating the Act...
Article Molecular dynamics simulations and drug discovery
Molecular Dynamics Simulation for All (https://www.cell.com/neuron/pdf/S0896-6273(18)30684-6.pdf)
Tutorial:
Protein Ligand Gromacs Tutorial by Justin Lemkul (http://www.mdtutorials.com/gmx/complex/index.html)
Protein-Ligand MD: GROMACS Tutorial- PART 1 https://youtu.be/PCsg4rBN6wg Protein-Ligand MD: GROMACS Tutorial- PART 2 https://youtu.be/lBT404qVBSY Protein-Ligand MD: GROMACS Tutorial- PART 3 https://youtu.be/fSDD6tEEWlo
RG Discussion Thread:
https://www.researchgate.net/post/After_protein_ligand_simulation_in_gromacs_how_do_we_analyze_the_simulations
I hope this helps you in understanding MD and analyzing your results.
GROMACS tutorials are goods for understanding. Aldo this paper may help you https://doi.org/10.1038/nsb0902-646
For basics you can read these pdf files. It may help you. You can also download the GROMACS manual from www.gromacs.org
http://www.mdtutorials.com/gmx/
https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0
Code GROMACS Normal Mode Analysis Script
Code GROMACS MD Analysis Script
Code GROMACS (AMBER)
Code GROMACS (CHARMM)
And then you can start and learn by yourself.
HTH!
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