AW: Regarding Temperature calculation from velocity trajectory of NAMD-2.9

From: Norman Geist (
Date: Thu Jul 10 2014 - 05:08:50 CDT

You didn’t consider the reduced degrees of freedom for constrained hydrogen due SHAKE aka rigidbonds ;)


Norman Geist.


Von: [] Im Auftrag von Shailesh Pandey
Gesendet: Donnerstag, 10. Juli 2014 11:30
Betreff: namd-l: Regarding Temperature calculation from velocity trajectory of NAMD-2.9


Dear NAMD users,

I have performed a MD simulation of a protein+ligand system with explicit solvent and PBC with NPT ensemble.

Now as one of the tests of equilibration, I want to look at temperature profile of Solvated system, protein+ligand, water, and center of mass of complex. As discussed in

Gallo, M. T., Grant, B. J., Teodoro, M. L., Melton, J., Cieplak, P., Phillips, G. N., & Stec, B. (2009). Novel procedure for thermal equilibration in molecular dynamics simulation. Molecular Simulation, 35(June 2014), 349–357. doi:10.1080/08927020802647272

And, we can calculate temperatures of different configurations if we have corresponding velocity trajectory.

I am using following tcl code to calculate temperature after loading psf file and velocity trajectory as molecule data

proc getTemp { frame } {
    set all [atomselect top all frame $frame]
    set eng {}; set esum 0;
    foreach m [$all get mass] v [$all get {x y z}] {
        set e [expr {0.5 * $m * [vecdot $v $v]}]
        lappend eng $e
        set esum [expr {$esum + $e}]
    set T [expr { $esum * 2.0 / (3.0 * [$all num] * 0.00198657) }]
    puts "frame: $frame ## Temp: $T"

I am following it from


It produces temperature in range of 220-230 for solvated system, but log file shows temperature fluctuating around 310, as 310K was the simulation temperature.

I am unable to find where I am doing wrong?

Any help in this regard is appreciated.

Thank you.

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