AW: Tempreture Profile along z axis

From: Norman Geist (
Date: Fri Jan 09 2015 - 02:23:04 CST

I have a program doing something similar, but with a selectable grid size in
all directions, results are plots per dimension (optional for various atom
types aswell) and a DX volume map for visualization. What I noticed there
was, that the temperature is always distributed all over the system with
very fast and very slow particles (boltzman distribution). So you need to
average a lot of frames to actually get smooth temperature values for your
slaps. But, unfortunately after all the effort to write the program I
notices that the outcome is actually _nothing_ as you will get the same
temperature for all your slaps, as maybe expected.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von Jim Phillips
> Gesendet: Donnerstag, 8. Januar 2015 17:49
> Betreff: Re: namd-l: Tempreture Profile along z axis
> Your cell is three times the size it should be for 4000 waters. Check
> the
> density that NAMD reports on startup. You've probably got some kind of
> shock wave going on depending on the initial distribution.
> Jim
> On Thu, 8 Jan 2015, JAVAD NOROOZI wrote:
> > Hi all,
> > I have devided an elongated box (z=180, x=y=45 and 4000 water
> molecule) into 20 slabs along the z axis to measure temperature profile
> in an NVT run.The temperature should be equal at each slabs (linear
> profile), but i see a large fluctuation from slab to slab. I tried to
> use different langevin damping coeff  and more water molecules, but no
> improvement.
> > Any idea?
> >
> >

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