temperature

Calculate system temperature using velocities of specified atoms.

temperature [<name>] [out <filename>] 
                {frame | 
                   [<mask>] [ntc <#>] [update] [remove {trans|rot|both}]
                }

[<name>] Data set name.
[out <filename>] File to write values to.
frame Do not calculate temperature; use existing frame temperature.
[<mask>] Atoms to calculate temperature for.
[ntc <#>] Value of SHAKE bond constraint: 1 – none, 2 – bonds to H, 3- all bonds (equivalent to SANDER/PMEMD).
[update] Update temperature in Frames with calculated temperatures.
[remove {trans|rot|both}] Correct for removed translational, rotational, or both kinds of degrees of freedom.

Calculate temperature in frame based on velocity information. If ‘update’ is specified, update frame temperature too. If ‘frame’ is specified just use frame temperature (e.g. read in from a REMD trajectory). The ‘ntc’ keyword can be used to correct for lost degrees of freedom due to SHAKE constraints (2 = bonds to hydrogen, 3 = all bonds). The ‘remove’
keyword can be used to account for removed translational and/or rotational degrees of freedom.

For example, if using a trajectory that has been generated with SHAKE on hydrogens, no periodic boundary conditions (i.e. no box), and has had the center of mass periodically removed:
temperature T1 ntc 2 remove both out T1.dat

If using a trajectory that has been generated with SHAKE on hydrogens, periodic boundary conditions (i.e. with a box), and has had the center of mass periodically removed:
temperature T1 ntc 2 remove trans out T1.dat

If using a trajectory that has been generated with SHAKE on all bonds, periodic boundary conditions, and no center of mass motion removal:
temperature T1 ntc 3 out T1.dat