I am trying to calculate lateral lipid diffusion via simulation in the xy direction . The method I used to calculate the diffusion is by calculating the gradient or slope of plot of MSD (mean square displacement) vs (time).
Here I attached a plot I got for MSD vs time.
But the plot I got shows some negative gradient or slope in the middle of the graph.
How one can explain this kind of plot?
I have some doubts if the plot is correct? Ask
Appreciate if I can get some guidance here.
note: ( I used AMBER to simulate my system)
Dear Abel, during the simulation I have used iwrap=1. But for MSD calculation I unwrap the trajectory. This what advised in the AMBER manual.
Hello Vijay,
I assume that unwrapping the trajectory means that AMBER tries to make the trajectory as smooth as possible by guessing if the particle was wrapped during the simulation (I am not an expert with AMBER). I know that in this case unwrapping can fail if the particles travel large distances between two trajectory points. Could this be the case here?
I suggest you compare the MSD with simulations using iwrap=0. If you still find a more or less flat MSD it means that your particles are not diffusing.
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