From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Tue Dec 15 2009 - 09:41:23 CST
... $PDBVELFACTOR * 1e-20 / 1e-24 / $NDOFs .....
oops, found the typo. Next time, I'll wait a night before sending these
questions out :-)
Sebastian
Sebastian Stolzenberg wrote:
> Dear All,
>
> As a test for some further reasons down the road, I am trying to
> reconstruct temperatures from a velocity binary file. Here is a script
> calculating the temperature:
>
> *************************
> set mykin 0.0
> set numatoms 0.0
> set PDBVELFACTOR 20.45482706
> set N_A 6.022142e23
> set k_B 1.38065e-23
> set NDOFs 578347
>
> foreach mymass {1.00800001621 12.0109996796 14.0069999695
> 15.9989995956 22.9897994995 30.9740009308 32.0600013733 35.4500007629} {
> set mysel [atomselect top "mass $mymass"]
> set numatoms [expr $numatoms + [$mysel num]]
> foreach mycoord {x y z} { set v($mycoord) [$mysel get
> $mycoord] }
> set v2sum($mymass) [expr [vecdot $v(x) $v(x)] + [vecdot $v(y)
> $v(y)] + [vecdot $v(z) $v(z)]]
> set mykin [expr $mykin + $mymass*$v2sum($mymass)]
> }
>
> puts [expr $mykin / 1000 / $N_A * $PDBVELFACTOR * $PDBVELFACTOR /
> 1e-20 * 1e-24 / $NDOFs / $k_B]
>
> *************************
>
> I obtained the value for $NDOFs from the log file ("578347 DEGREES OF
> FREEDOM").
>
>
> Checking with the log file, I get the correct temperature value - only
> that it is off by exactly 8 orders of magnitude!
>
> What (orders of magnitude) am I missing in my conversion? Maybe a
> fresh eye can help here? I am using NAMD 2.7
>
> Thank you,
> Best,
> Sebastian
>
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