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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