From: Norman Geist (norman.geist_at_uni-greifswald.de)
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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Shailesh Pandey
Gesendet: Donnerstag, 10. Juli 2014 11:30
An: namd-l_at_ks.uiuc.edu
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 http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node14.html
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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