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

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Jul 11 2014 - 02:51:44 CDT

Seriously? A contrained hydrogen does only have 2 not 3 DOF. And for TIP3P water each atom has only 2DOF.

 

Therefore:

 

#rigidbonds none=0; water=1; all=2

proc getTemp { frame rigidbonds } {
    set all [atomselect top all frame $frame]
    set eng {}; set esum 0; set nDoF 0;
    foreach m [$all get mass] v [$all get {x y z}] id [$all get index] {
        set e [expr {0.5 * $m * [vecdot $v $v]}]
        lappend eng $e
        set esum [expr {$esum + $e}]

       set all [atomselect top all frame $frame]

          set DoF 3.

          #SHAKE?

          set c1 [atomselect top "index ${id} and ((type 'HW' or hydrogen) or water)" ]

          set c2 [atomselect top "index ${id} and water" ]

          if { $rigidbonds == 2 && [$c1 num] > 0 } {

              set DoF 2.

          } elseif { $rigidbonds == 1 && [$c2 num] > 0 } {

              set DoF 2.

          }

          $c1 delete

          $c2 delete

          incr nDOF $DoF
    }

    set T [expr { $esum * 2.0 / ($nDoF * 0.00198657) }]
    puts "frame: $frame ## Temp: $T"
}

 

Von: Shailesh Pandey [mailto:shaileshp51_at_gmail.com]
Gesendet: Donnerstag, 10. Juli 2014 16:30
An: Norman Geist
Betreff: Re: namd-l: Regarding Temperature calculation from velocity trajectory of NAMD-2.9

 

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

 

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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