Hi, all.
I hope this email finds you well. I am reaching out to inform you that I am currently undertaking a molecular dynamics (MD) simulation of a tuberculous protein complexed with a drug. The primary objective of this simulation is to evaluate the stability of the interaction between the drug and the protein, with the aim of assessing its potential as a lead compound.
The simulation is planned for a duration of 50 nanoseconds, employing a time step (dt) of 0.002. I intend to perform a comprehensive analysis of various parameters to gain insights into the system dynamics. Specifically, I am interested in monitoring the Radius of Gyration (RoG), Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and hydrogen bonding throughout the simulation. Additionally, I plan to conduct MMPB/GBSA calculations.
Considering the diverse timescales of these analyses, I would appreciate your guidance on how often I should save frames to the trajectory file to ensure a robust and meaningful analysis. Your expertise and insights will be invaluable in optimizing the simulation setup for obtaining reliable results.
Thank you for your time, and I look forward to your advice.
Regards,
Dr. Kaleem Arshad
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Received on Fri Feb 23 2024 - 22:00:02 PST
