have you tried cpptraj in ambertools 17 yet?
Hai
On Fri, Jul 28, 2017 at 12:37 AM, Meng Wu <wumeng.shanghaitech.edu.cn>
wrote:
> 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 - 22:00:03 PDT
