[gmx-users] Distance between the atoms greater than Box length

[Dilip.H.N]

Hello all,
I have extracted the trajectory of my system containing all the water
molecules and my box length is 2.48 ~2.5 nm.

And i have written a code which calculates the inter-atomic distance (in my
case it is inter oxygen distances). And when i calculate it (using the
distance formula ie.,
{sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
of say
6SOL     OW   13   2.405   0.185   1.774
    6SOL    HW1   14   2.452   0.097   1.782
    6SOL    HW2   15   2.466   0.259   1.804
    7SOL     OW   16   0.016   2.177   0.277
    7SOL    HW1   17   0.098   2.141   0.234
    7SOL    HW2   18  -0.064   2.126   0.245


---
With Best Regards,

Dilip.H.N
PhD Student.
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06/04/18,
5:15:08 PM