Molecular Dynamic Simulation Process: Part III

The analysis of MD simulation results was discussed in this lecture. It mainly includes visualization of trajectories, RMSD, RMSF, Hydrogen bond analysis, dihedral angle analysis, Principal component analysis, Essential dynamics, Free energy landscape, Normal mode analysis.

[@gizachewdiga]

This is the best lecture. From the lecture, we are able to identify Monte Carlo simulation and Molecular dynamics, Molecular dynamics, energy minimization& localization (alternative to DFT), a method of data analysis using molecular dynamic simulation, a method of determining root mean square deviations, its application in simulating and modeling protein structure and conformation, and bioinformatics, workflow in protein, conversion of trajectory file to PDB file for protein ( I think it is also possible to apply for most polymers), Free energy landscape(Gibbs energy landscape), Bio 3d Program package, 3D plot using Python, Mode visualization of proteins and Elastic Network Model (Mesophilic & Thermophilic network model), displacement plot, Nature of loop movement in Protein, and NMA Movie. Thanks!

[@suruchibhambri_3599]

Great explanation sir but one request can you please also provide the command for the analysis

[@sagarkamble2947]

Very helpful.Thank you.

[@Nature_joys]

Thank you sir

[@RameshKumar-cm1cg]

🥰☺

[@moulayahfidelalaouy810]

please sir can you give an example of the curves of rmsd, rmsf, ​​sasa and Rg with the interpretation

[@rikganguly5886]

Sir how to merge pc1 and 2 in pymol

[@moulayahfidelalaouy810]

It's a fun course but unfortunately I have a problem with English