Dear All,
I have simulated a micelle in the water with Amber16, but when I tried to re-image the trajectory usimg autoimage (I also tried image center familiar), I found it's hard to get all the micelle molecules in a box, I mean there were always a few molecules outside the box. My micelle is in a sphere and I want to see how its radius changes over time, so I would like to analysis its radius of gyration using 'radgyr', but the problem is I'm not sure if the above-mentioned PBC problem will affect my calculation of the Rg of the micelle including all molecules. If yes, how could I solve the PBC problem?
Any suggestions would be greatly appreciated.
Thank you in advance!
All the best,
Wu Meng
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Received on Thu Jul 27 2017 - 22:00:02 PDT
