How to choose the best structure from the trajectory file after doing a Molecular dynamics simulation of 30ns or any for particular time interval?

Question

[sweetpharma88]

I have done a molecular dynamics simulation for a complex (which includes ligand and the Protein) for 30ns. And now I want to get the best structure with least minima from the trajectory obtained after doing the MD run. Could anyone please tell me what is the correct procedure to get the best representative structure from the trajectory file.

Can i take the last frame as the best structure frame which is having the least energy score?

Answer 1

[João Rodrigues]

Molecular dynamics is not energy minimization, so taking the last frame does not necessarily assure the lowest energy of the trajectory. If you want to do so, analyze the energy of the system over the trajectory and take the structure from that time frame.

What is probably a better alternative is to cluster your trajectory and then take the centroids of the most populated clusters as representatives. One structure won't be representative of your trajectory.