**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Sat Nov 07 2009 - 16:55:13 CST

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On Sat, 2009-11-07 at 17:31 -0500, Sebastian Stolzenberg wrote:

*> > 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.)
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*> Sweet, so please let me understand the logic of "n_DOF=3n-3":
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*> for the DOFs, we have
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*> 3 for overall translations
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*> 3 for overall rotations
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*> and 3n-6 for the fundamental oscillations
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nope. we don't have those. we treat our system

as N individual point particles. the 3N-6 for

oscillations only holds for crystals/lattices/etc.

there you have the 3n DOFs minus translation and rotation.

*> Since we only consider kinetic energies for the temperature, we do not
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*> count the fundamental oscillations twice.
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*> Then, n_DOF=3n-3 because we can ignore the 3 translation DOFs (change of
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*> reference frame).
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*> Why not also ignoring the 3 overall rotations to get 3n-6? Maybe it
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*> doesn't matter because
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*> 3n-3 ~ 3n ~ 3n-6, since 3n is large....
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with PBC you are only invariant against translations of

your total system.

*> 2.)
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*> Too bad though I am using shake. Fixed bonds reduce the DOFs, so how
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*> does NAMD calculate n_DOF then?
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very simple: each "shaken" bond or angle is equivalent to

removing one DOF. so waters have 6 DOFs instead of 9. if

you go to more complex constraints it can become very complicated.

i don't know how much care NAMD takes for those. last time i

looked into these issues with more detail was with an ab

initio MD code, where this matters much more, than in typical

NAMD calculations.

*> By the way, is there a nice TCL script/NAMD trick calculating T from the
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*> velocities, or would I need to dig into the source code to see how this
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*> is done and write some code myself?
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the coding here is extremely simple, except for having to know

which bonds/angles are shaken (and not stirred) and particularly

how to handle the situation of computing the instantaneous temperature

if only part of a constraint (one atom of a constrained bond, one or

two atoms of a constrained angle and so on) is in the group of atoms

where you want to monitor the temperature.

as usual, the ultimate answer is the source code.

cheers,

axel.

*>
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*> Thank you very much,
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*> Sebastian
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*>
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*>
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-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com Institute for Computational Molecular Science College of Science and Technology Temple University, Philadelphia PA, USA.

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