I have performed molecular dynamics simulation for 100 ns for 6 ligands. I would like to know how many frames to use for MMPBSA analysis?
Should I check the RMSD plot for each of them, identifying the more stable time interval and run the MMPBSA analysis for only that part?
Or should I define a common time interval for all six complexes to maintain consistency?
keep consistent for sampling of frames (Interval i.e., every 10th or 100th frames) over all 6 ligands. Look gmx_qk for more information about reducing frames from trajectory. (Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...
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You can perform MMGBSA calculations on the entire trajectory; however, this would be highly time-consuming. To optimize computational efficiency, you may consider extracting frames at intervals of every 10th or 100th frame, depending on your specific requirements and the computational resources available. You can refer to this site https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/
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