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Re: [ESPResSo] Langevin Thermostat

From: Axel Arnold
Subject: Re: [ESPResSo] Langevin Thermostat
Date: Tue, 8 Jun 2010 10:15:58 +0200
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On Monday 07 June 2010 17:27:31 Mikheil Azatov wrote:
> Hi,
> I'm modeling polymer system in Lnagevin thermostat. To start I reduced my
> system to just 2 particles in Langevin thermostat. When I'm visualising my
> results I receive something very weird. The particles just jump from point
> in the space to another. I tried it with different number of particles with
> or without interactions between them and the results are always the same(
> No continuous type of motion , particles just jump from one place to
> another). As I understand I should receive brownian type of motion instead
> of these random huge jumps of particles. If anyone had this kind of problem
> please help me.

In fact, due to your rather large damping constant of 2 and the really small 
time step, you should observe practically no motion. However, Espresso by 
default sends folded coordinates to VMD, and your particles are placed exactly 
at the origin of the simulation box. Therefore, they appear to hop from time 
to time to the other end of the simulation box.

If you use "imd positions -unfolded", the itinerant unfolded positions are 
sent to VMD. In this case, you observe really no movement. However, if you 
want to simulate a whole melt of polymers, that is not a good solution - with 
time, the polymers drift out of the primary simulation box, which makes the 
melt appear more and more dilute. A compromise is to fold the polymers 
according to their center of masses - look at the PBC tools of Olaf how to do 
that with VMD.


JP Dr. Axel Arnold Tel: +49 711 685 67609
ICP, Universit├Ąt Stuttgart      Email: address@hidden
Pfaffenwaldring 27
70569 Stuttgart, Germany

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