You first need to obtain an .xtc in which the micelle is entirely within the unit cell in every frame:
http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering You can then use g_gyrate to get the radius of gyration or g_rdf to get the radial distribution function from the micelle COM or some other tool compute the diameter (but note that there are many ways to define the "diameter" of an object with a rough surface). Chris. -- original message -- I am working with an emulsion water/n-dodecane in a box of 29nm. I wish to know how I can to get the diameter of the micelle in the frame, then I need to measuring the average diameter of the micelle in each frame. Thanks for your help!!
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