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Re: [ESPResSo-users] Sistematically decreasing of Temperature with DPD t

From: Salvador H-V
Subject: Re: [ESPResSo-users] Sistematically decreasing of Temperature with DPD thermostat
Date: Wed, 15 Jan 2014 10:00:20 -0600

Hi Stefan,

In all the simulations I am using:

i) 2dim system periodic 1 1 0
ii) blx bly blz = 2.5*diam
iii) Generalized LJ potential to mimic hard core interaction

First simulations I was using:
i) rigid bond command for the dimers (dumbbells) => No virtual sites
ii) Langevin Dynamics Thermostat

Current Simulations I will try:
i) Harmonic Bonds with high K value (but temperature seems to be dependent of such value!)
ii) DPD thermostat

I want to reproduce (qualitatively) some experimental results. So, I am really interested in performing the simulations with the correct parameters and methodologies.

In your email you mentioned: "bond length constraint thing... should be a RATTLE or SHAKE implementation. I'm not exactly sure how it works and I'm not sure if it works..."

This means that using rigid bonds or even harmonic bonds in a 2Dimensional system is not a good idea? 

When I used rigid bond command, I was able to reproduce some structural properties and the system "looks fine".  The lentgh bond is keeped constant, temperature is preserved and total energy is almost just kinetic energy. However I am interested in dynamical properties... 

I would really appreciate any advice or suggestion.  

Thanks a lot


On Wed, Jan 15, 2014 at 9:33 AM, Stefan Kesselheim <address@hidden> wrote:
Dear Salvador,

On Jan 15, 2014, at 4:11 PM, Salvador H-V <address@hidden> wrote:

> And now the temperature is fluctuating around 1.6$$... I had to use a very high value of K to keep the particle's center distance around 1.0.

OK. This means you script is not terribly buggy :-).

> So, I have to think more carefully what Stefan said: "Thermalization of rotational degrees of freedom is entirely different in Langevin than what happens when combining rigid bodies with DPD (this so far probably nobody has done)."

Let me ask you briefly one thing: Did you use rigid body dynamics with virtual sites or did you use the bond length constraint thing. The second should be a RATTLE or SHAKE implementation. I'm not exactly sure how it works and I'm not sure if it works or anyone has tried  it. Anyone?



Dr. Salvador Herrera-Velarde
Simulacion Computacional de Materia Condensada Blanda
Sub-Direccion de Investigacion y Posgrado
Instituto Tecnologico Superior de Xalapa (ITSX)
Instituto Tecnológico Superior de Xalapa
Sección 5A Reserva Territorial s/n, 
Col. Santa Bárbara, 
CP 91096
Xalapa, Ver. Mexico


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