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Re: [ESPResSo-users] Simulation of a polyelectrolytes system.

From: Stefan Kesselheim
Subject: Re: [ESPResSo-users] Simulation of a polyelectrolytes system.
Date: Fri, 2 Sep 2011 01:30:59 +0200

Hello everybody,

before taking part in the discussion, I would like to remind everybody that 
this mailing list has mainly served the purpose to discuss Espresso issues that 
are not clearly documented or not working, or where it not clear how to make 
them working. Thus the focus has been on the technical side. 
This also includes that basic questions of molecular simulations  are not to be 
answered here, where busy people would spend their rare time to reply on 
questions that are (maybe better) described in text books on that topic, and 
also that basic descriptions of more advanced or recent algorithm are not 
described here, but in the corresponding publications. 

Am 01.09.2011 um 18:29 schrieb Owen Hickey:

> I believe currently it is only implemented
> for a constant force on particles but I am guessing it wouldn't be too
> hard to change it such that the external force varies with time.

I have been working with the LBM for quite some time now and I have realized 
that it takes quite some time that the flow field around a particle that 
subject to a force has enough time to form. The corresponding timescale is 
L^2/\nu where L is the box length of the system and \nu the kinematic viscosity 
of the system. This can be of order 10 if common units are chosen (box of order 
10, LJ sigma 1, viscosity of order 1 ...). This then corresponding to at least 
1,000 MD steps and thus it is computationally cheap enough to vary the external 
field just by update the external force on each bead often enough.

setmd time_step 0.01
for { set i 0 } { $i < 100 } { incr i } {
  part 0 ext_force [ expr [ part 0 print q ] * sin(2*3.1415 * $i / 100 ] 0 0
  incr 100

muE can be changed accordingly.

And finally: Writing to mailing lists and addressing not the community usually 
answering to questions, but single persons is nothing I personally consider 
very polite.

Cheers and good luck

> Hope that helps,
> Owen
> On Thu, Sep 1, 2011 at 11:40 AM, Chunda Zhou <address@hidden> wrote:
>> Dear Dr. Holm,
>> I am a graduate student in biophysics. We conduct a series experiments which
>> show DNA collapses under A.C. electric field.  ( Collapse of DNA in ac
>> Electric Fields, in the attachment. )
>> We are now using general ESPResSo to simulate. But according to the mail
>> list, in the general ESPResSo could only set the velocity for all the
>> charged particles as one value muE. In your paper Mesoscale modelling of
>> polyelectrolyte electrophoresis, you have measured the relation between
>> velocities and electric field with ESPResSo. I think you are the only person
>> who can do this. Could you please show us more information on this?
>> Best wishes,
>> Chunda Zhou
>> Department of Physics
>> 919-995-5631

Stefan Kesselheim
Institute for Computational Physics
University of Stuttgart

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