[gmx-users] questions about trjorder

[Yunfeng Hu]

Hi, I am trying analyze the distance change between a ligand atom and 
the surrounding waters. I first used make_ndx (> 12 & a 2391) to define 
this atom and then use trjorder to generate a pdb file that includes 
all the "reordered" water molecules besides the protein and the ligand. 
As the manuscript claims that the last column of this pdb file 
represents the referred distance. However the distance between atom 
24326 OW and atom 2391 C2 is 3.55 angstrom. What does 1.79 stand for 
here then?


...
ATOM   2391  C2  COC B 231      45.060  26.510  31.730  1.00  0.00
...
ATOM  24326  OW  SOL  7541      47.780  25.420  29.720  1.00  1.79
ATOM  24327  HW1 SOL  7541      47.810  24.520  29.290  1.00  1.85
ATOM  24328  HW2 SOL  7541      47.040  25.450  30.390  1.00  1.79
ATOM  24116  OW  SOL  7471      47.180  23.510  32.240  1.00  2.04
ATOM  24117  HW1 SOL  7471      46.480  24.060  31.770  1.00  1.96
ATOM  24118  HW2 SOL  7471      46.950  23.430  33.210  1.00  2.10
ATOM  24128  OW  SOL  7475      48.780  27.900  29.550  1.00  1.63

Thanks!

Eric