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Re: [ESPResSo-users] DPD

From: Jiajia Zhou
Subject: Re: [ESPResSo-users] DPD
Date: Thu, 11 Sep 2014 09:48:36 +0200

On Wed, Sep 10, 2014 at 9:52 PM, Ulf Schiller <address@hidden> wrote:
> On 09/10/2014 07:02 PM, Dudo wrote:
>> On Wed, Sep 10, 2014 at 7:09 PM, Christoph Junghans <address@hidden
>> <mailto:address@hidden>> wrote:
>>     2014-09-10 9:08 GMT-06:00 Dudo <address@hidden
>>     <mailto:address@hidden>>:
>>     > Please,
>>     >
>>     > should I generate additional particles for using the DPD thermostat?
>>     I don't really understand why you would do that. Can you give some
>>     details about the problem you are studying?
>> Hi Chris,
>> well, what I would like to do is to drag a polymer molecule through media,
>> with a constant velocity with respect to the media as possible.
>> Hence, even if I fill the periodic box with a huge number of "solvent"
>> bodies it would start moving as one phase after some time.
>> So this is not the way.

One way to get around this, at least for me in the colloid case, is to apply an
equal amount of force in the opposite direction, and the force is distributed to
all the solvent DPD beads. In this way, the total force on the system is still
zero. Of course one has to measure the flow velocity which sets the frame
of reference.

> But that is physical. Assuming you intend to drag the molecule by
> applying a force, this will 'pump' momentum into the system which will
> diffuse according to the viscosity of the medium. Unless you dissipate
> momentum by some means (e.g. walls), the whole system will accelerate.
> If you stop applying the force at some point, velocity gradients will
> decay while total momentum of the system is conserved.
>> What I would like to see coming from my simulation, is at first the
>> molecule orienting with its lowest energy/lowest friction or
>> hydrodynamic radius profile with respect to the direction of the
>> movement through the media, with the molecule started re-shaping after a
>> while..
> This sounds like you intend to look at the response of the molecule to
> an external flow. In that case, you need to decide first what kind of
> flow you would like to impose. Simple examples might be uniform, linear
> or parabolic flow profiles. However, if you are merely interested in the
> mobility tensor of the molecule, you may be able extract it from
> equilibrium simulations by means of linear response theorems (keep
> finite size effects in mind for a periodic system).
> Note that such properties have been studied extensively for various
> kinds of polymers (linear chains, stars, rings), and you may want to
> take a second look at the available literature.
> Best wishes,
> Ulf
> --
> Ulf D. Schiller
> Centre for Computational Science
> University College London
> 20 Gordon Street
> London WC1H 0AJ
> United Kingdom

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