[gmx-users] Re: temperature

[Roy]

Mark,

According to the manual, the temperature of a group should always be
calculated from the total KE of the group (see eq 3.13 in the manual), which
presumably includes  contributions from the translational motion of the
center of mass of the group, plus the rotational motion around the center of
mass of the group, plus any random non-rigid motion within the group. 
However, according to appendix D.72 for g_traj, the option –ot plots the
temperature of each group calculated only from the rigid body translational
velocity of the center of mass of the group, since the command –ot implies
–com. Aren’t these two definitions of temperature incompatible, since the
–ot definition ignores two terms (rotational and random)?
  
Roy


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