[gmx-users] water sorient

xy21hb xy21hb at 163.com
Mon Dec 7 13:06:49 CET 2015

Dear all, I would like to calculate the water orientation near ubiqutin by gmx_sorient, gmx sorient -f md.trr -s md.tpr -o -no -ro -co -rc

first, the sord.xvg shows the angle (i.e. theta 1) between the vector1 (nearest heavy protein atom to water oxygen) and
vector 2 (water oxygen to the mid of of water hydrogen 1 and 2) is mostly 90 degrees, isn't that weird?
I would expect water dipole more or less pointing to or away from the vector 1, depending on the charge of the heavy atom.

2nd, sori.xvg second column should be the distribution of cos (theta1), but it shows some value greater than 1.

Any ideas?



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