Issues faced using Energy2d function

[GSINGH006]

Hi ,@clonker while using deeptime.util.energy2d for plotting 2d energy landscape i faced some issues .I am backbone_torsions(cossin=True) as feature and when i am generating energy landscape with x-axis as TIC1 and y axis as TIC2 I am generating it by using tica lag time=400 ps But when i use lag time=800 ps the plot completely shifts like its an mirror image of earlier plot(400 ps).I am not able to understand this behaviour ?

[clonker]

It is very hard to say what is going wrong without seeing the actual plot. Keep in mind, though, that by changing the lagtime, you are also changing the operator you are approximating. It might very well be, that the processes found under 800ps are different onces compared to 400ps. I recommend looking at the implied timescales and seeing whether there is a separation of scales.

[GSINGH006]

@clonker here are the Implied timescale plot and timescale separation plot when 800 ps was taken as msm lag time there is time scale separation

[GSINGH006]

hi @clonker i still couldn't figure out the reason behind shifting of plots.I have attached the pictures of the free energy landscape for 400 ps and 1000 ps lag time

[clonker]

It looks to me like it is just mirrored which is fine as long as the general shape is preserved. The important part is the general shape according to the dominant axes. Think about, e.g., PCA. There mirroring the image while preserving the general shape and axes is also fine, it just means the projection is a bit different.