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

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

**Next message:**Sebastian Stolzenberg: "Re: temperature calculations from velocities in NAMD?"**Previous message:**Sebastian Stolzenberg: "Re: temperature calculations from velocities in NAMD?"**In reply to:**Sebastian Stolzenberg: "Re: temperature calculations from velocities in NAMD?"**Next in thread:**Sebastian Stolzenberg: "Re: temperature calculations from velocities in NAMD?"**Reply:**Sebastian Stolzenberg: "Re: temperature calculations from velocities in NAMD?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

*> > the iffy part is often to determine the exact number of DOFs.
*

*> > without shake this is usually 3n-3.
*

*> >
*

*> 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
*

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
*

*> 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....
*

with PBC you are only invariant against translations of

your total system.

*> 2.)
*

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

*> does NAMD calculate n_DOF then?
*

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
*

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

*> is done and write some code myself?
*

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.

*>
*

*> Thank you very much,
*

*> Sebastian
*

*>
*

*>
*

-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com Institute for Computational Molecular Science College of Science and Technology Temple University, Philadelphia PA, USA.

**Next message:**Sebastian Stolzenberg: "Re: temperature calculations from velocities in NAMD?"**Previous message:**Sebastian Stolzenberg: "Re: temperature calculations from velocities in NAMD?"**In reply to:**Sebastian Stolzenberg: "Re: temperature calculations from velocities in NAMD?"**Next in thread:**Sebastian Stolzenberg: "Re: temperature calculations from velocities in NAMD?"**Reply:**Sebastian Stolzenberg: "Re: temperature calculations from velocities in NAMD?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:51:39 CST
*