How to analyse data after gromacs simulation of protein?

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Rajan Kumar Choudhary Popular answer

SEND ME YOUR MAIL ID I CAN SEND YOU SOME USEFUL COMMANDS.FIND THE ATTACHMENT

Justin Lemkul

There is no magic recipe for analysis. The types of analysis you perform depend on the question(s) posed before even doing the simulation. What did you hope to observe? What hypothesis were you testing by doing the simulation?

Sangita Kachhap

Hi Sunil

There is no any step by step protocol for analysis after MD simulation it depends on your question for what your are doing MD. There are so many basic analysis that you you must do like calculation of RMSD, RMSF and radius of gyration of your trajectory generated during MD simulation to check, is your trajectory stable during MD simulation? It will also tell you effect on your protein due to any mutation in your protein or binding of ligand. In addition to these you can do interaction analysis (within protein/ protein-ligand), secondary structure analysis. So first go for tutorial and literature regarding your problem and them do it for your protein.

Nubia Prates

A start would be to look for articles in which they have analysis of molecular dynamics simulation. This website is very interesting.

http://nmr.chem.uu.nl/~adrien/course/molmod/analysis1.html

Rajan Kumar Choudhary

Srikanth Jupudi

Same question from me to analyze protein-ligand interactions in Gromacs.

Sourav Pal

hi all, i also faced same problems. i already did protein-ligand simulation tutorials in gromacs, now i want to calculate the RMSD calculation of complex and hydrogen bond stabilization and radius of gyration. so please anyone can give me the suggestion?

http://nmr.chem.uu.nl/~adrien/course/molmod/analysis1.html.....IS GOOD FOR ALL THE BEGINNERS AS Nubia Prates SUGGESTED

Some more useful files for beginners, I hope it will be helpful for you all. Let me know if you need my help.........Always happy to help

Mohamed AbdElAziz Khamis

https://www.researchgate.net/post/After_protein_ligand_simulation_in_gromacs_how_do_we_analyze_the_simulations

https://www.researchgate.net/post/Analysis_of_MD_Simulation_results

https://www.researchgate.net/post/Analysis_of_gromacs_results

https://arxiv.org/pdf/0912.0893