On 17/04/2012 7:32 AM, Roy wrote:
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)?
While g_traj -h says that g_traj -ot implies g_traj -com, I don't think
this means that the temperature is necessarily calculated from the
velocity of only the COM. Rather, I would expect that -ot calculates the
temperature from the full KE and simply reports the velocity for the COM.
You can test this with g_traj on a .gro file for a small group of atoms
for which you can construct a zero COM motion and non-zero full KE.
Mark
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