[gmx-users] wrong distances with g_dist

Dmytro Kovalskyy kovalskyy at uthscsa.edu
Tue Jun 26 23:14:31 CEST 2012


I try to calculate distance between two atoms with g_dist. Somewhat I get 
distance lower than actual.
Here there are coordinates of the two atoms (PDB format)
ATOM    702  CZ  ARG X  45       5.930   9.230  41.740  0.00  0.00
ATOM   2751  CA  PHE X 177      41.710  45.000  27.180  0.00  0.00

And the distance I get from g_dist is 4.6260725 nm while the actual is 5.265 

What the problem can be?


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