[gmx-users] temperature of a single water molecule

[Ali Mohyeddin]

Dear all,

I am going to calculate the temperature of single water molecule around a
protein by writing a simple script to calculate the temperature from
what "trjconv"
command prints out:

  mass vx vy vz
2SOL OW 16 0.2789 -0.4959 0.8134
2SOL HW1 1 1.0917 1.3308 0.0835
2SOL HW2 1 0.1324 1.9991 -0.6413






I set the "constraints = none" in mdp file. When I consider 9 DOF to
calculate the temperature,  it is a different T than what "gmx energy"
gives when I define a energy group for a single water molecule.

Any response for the reason would be appreciated.

Mohyeddin