AMBER Archive (2009)

Subject: [AMBER] MSD of ligand??

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HI
MSD = mean square displacement
diffusion coefficient = d/dt (MSD)

I simulate the protein and ligand system and then calculate the MSD of the ligand.
Then, i drew the plot of the time evolution of the MSD.
But the the MSD decreases as time for some period.

I see nothing about my codings.
Would you please tell me about any possible errors i made?
Thank you
Lin

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• Previous message: Jason Swails: "Re: [AMBER] non standart residue library creation with tleap (Zn atom)"
• In reply to: Carlos Simmerling: "Re: [AMBER] Increase Temperature to 550 K"
• Next in thread: Chih-Ying Lin: "[AMBER] The decreasing MSD of ligand??"
• Next in thread: FyD: "Re: [AMBER] Increase Temperature to 550 K"
• Reply: Chih-Ying Lin: "[AMBER] The decreasing MSD of ligand??"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]