Hi<br>The MSD decrease occurs in the long times.<br>The ligand has bounded to a protein.<br>How can the decrease happen?<br><br><br>Thank you<br>Lin<br>
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Chih-Ying Lin wrote:<br>
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> HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I<br>
> simulate the protein and ligand system and then calculate the MSD of the<br>
> ligand. Then, i drew the plot of the time evolution of the MSD. But the<br>
> the MSD decreases as time for some period. I see nothing about my<br>
> codings. Would you please tell me about any possible errors i made?<br>
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MSD can decrease due to insufficient sampling (time of the simulation, number of<br>
frames analyzed, etc). Depending on what you define as "some period" (during<br>
the initial part of the simulation? the middle? the end?) the behavior may or<br>
may not be normal, but from the few details you provide, there's no way to know.<br>
What do you hope to see in this analysis? Will a ligand bound to a protein<br>
really diffuse that much anyway?<br>
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-Justin<br>
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> Thank you Lin<br>
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