Hello,
I am trying to visualize and calculate the displacement of a certain type of lipids within a membrane using the streamlines(2D) function in MDAnalysis https://www.mdanalysis.org/docs/documentation_pages/visualization/streamlines.html
To do so, I have prefiltered the lipids trajectory using a low pass filter (gmx filter -f lipids.xtc -all -ol lowpass.xtc ; gmx trjconv -f lowpass.xtc -pbc atom -o system -s lipids.gro ; gmx trjconv -f system.xtc -pbc whole -o low_pass.xtc -s lipids.gro) as explained on the "Flows" webpage here: http://sbcb.bioch.ox.ac.uk/flows/preprocess.html#preprocess
I then load the trajectory and coords and pass it to the function using the following:
u1, v1, average_displacement, standard_deviation_of_displacement =
MDAnalysis.visualization.streamlines.generate_streamlines(path+COORDS, path+TRAJ,
grid_spacing=10, MDA_selection='name P3', start_frame=400, end_frame=500,
xmin=5, xmax=85,
ymin=5, ymax=85,
maximum_delta_magnitude=15.0, num_cores=32)
The function seems to run fine and effectively returns the arrays u1 and v1 with dimensions complying the x/ymax-x/ymin/grid_spacing and the average and std but always zero.
I cannot tell what I am doing wrong. Maybe I am choosing the wrong xmin/xmax and ymin/ymax? My lipids span approximately 8 nm in x and y and to me it seems like the values of 5 and 85 for xmin/ymin and xmax/ymax would include most of the membrane in it?
I would appreciate if anybody would be able to help with this. I am also uploading the trajectory and the coordinate files for eventual testing.
Thanks in advance!
Cheers,
Davide
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