From: Shailesh Pandey (shaileshp51_at_gmail.com)
Date: Thu Jul 10 2014 - 09:31:03 CDT
---------- Forwarded message ----------
From: Shailesh Pandey <shaileshp51_at_gmail.com>
Date: Thu, Jul 10, 2014 at 7:59 PM
Subject: Re: namd-l: Regarding Temperature calculation from velocity
trajectory of NAMD-2.9
To: Norman Geist <norman.geist_at_uni-greifswald.de>
Yes, I am using rigidBonds water, how reduction in D.F is to be taken into
account?
On Thu, Jul 10, 2014 at 3:38 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> 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
> <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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