**From:** Sebastian Stolzenberg (*s.stolzenberg_at_gmail.com*)

**Date:** Sat Nov 07 2009 - 16:31:48 CST

**Next message:**Axel Kohlmeyer: "Re: temperature calculations from velocities in NAMD?"**Previous message:**Fred (Rui FENG): "Re: Is it a bug? TCL Script may Lead to Overflow"**In reply to:**Axel Kohlmeyer: "Re: temperature calculations from velocities in NAMD?"**Next in thread:**Axel Kohlmeyer: "Re: temperature calculations from velocities in NAMD?"**Reply:**Axel Kohlmeyer: "Re: temperature calculations from velocities in NAMD?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Thank You, Axel,

*> try a text book on MD (or stat mech) instead. the temperature of
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*> a group of particles is usually computed from its kinetic energy
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*> and the available degrees of freedom:
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*>
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*> T = Sum_i (m(i)*v(i)^2) / (n_DOF*k_B)
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*>
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*> the iffy part is often to determine the exact number of DOFs.
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*> without shake this is usually 3n-3.
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*>
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1.)

Sweet, so please let me understand the logic of "n_DOF=3n-3":

for the DOFs, we have

3 for overall translations

3 for overall rotations

and 3n-6 for the fundamental oscillations

Since we only consider kinetic energies for the temperature, we do not

count the fundamental oscillations twice.

Then, n_DOF=3n-3 because we can ignore the 3 translation DOFs (change of

reference frame).

Why not also ignoring the 3 overall rotations to get 3n-6? Maybe it

doesn't matter because

3n-3 ~ 3n ~ 3n-6, since 3n is large....

2.)

Too bad though I am using shake. Fixed bonds reduce the DOFs, so how

does NAMD calculate n_DOF then?

By the way, is there a nice TCL script/NAMD trick calculating T from the

velocities, or would I need to dig into the source code to see how this

is done and write some code myself?

Thank you very much,

Sebastian

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