# Re: temperature from binary velocities file

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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