If you plan post-processing, then more snapshots can reduce noise as long
as you have sufficient space. 1 frame per ps is probably reasonable.
On Sat, Feb 24, 2024, 12:39 AM Kaleem Arshad via AMBER <amber.ambermd.org>
wrote:
> 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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>
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Received on Sat Feb 24 2024 - 06:30:02 PST
