Re: Tempreture Profile along z axis

From: Jim Phillips (
Date: Thu Jan 08 2015 - 10:48:58 CST

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.


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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