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Re: [ESPResSo-users] Suddenly energy increases alot

From: roya moghaddasi
Subject: Re: [ESPResSo-users] Suddenly energy increases alot
Date: Fri, 21 Mar 2014 05:18:53 -0700 (PDT)

Hi dear Axel,
Thank you for your answers, they help me a lot.
I have a question about your last answer, how can I set up a polyelectrolyte as a tilted straight line? I use the followings in order to set up my polyelectrolytes :

polymer 1 $num_monomers_per_polymer 1.0 start $first pos $x $y $z mode RW charge -1.0 distance 1 types 0 0 FENE 0 constraints

part $first fix 1 1 1
What should I change to make them tilted straight lines?

My second question is, what do you mean by there is no need to warm_up, then? Isn't there any need to warm up the LJ interactions between just polyelectrolytes or LJ polyelectrolytes between polyelectrolytes and the cylinder?
Thank you,

On Thursday, 20 March 2014, 0:49, Axel Arnold <address@hidden> wrote:

provided that your box is large enough (at least box is 52**3, to hold
the cylinder), the polymers are in fact quite dilute. You could just set
them up as tilted straight lines starting from their mounting points,
thus avoiding any overlap. Then you don' t need to warmup and should
never encounter large energies.


On 19.03.14 16:31, Stefan Kesselheim wrote:
> Dear Roya,
> On Mar 19, 2014, at 4:24 PM, roya moghaddasi <address@hidden> wrote:
>> Dear Stefen,
>> Thank you for your reply,
>> My potentials are FENE, Coulomb(after warm_up), LJ 6-12 between particles, LJ 3-9 between particles and constraint.
>> The error " constraint violated by particle ...." constantly occured in my system, so I had emailed to the mailing list and some one in your group said that I should at first use the reflecting constraint and after warm_up delete and redefine the constraint without reflection and in this way I solved my problem. I don't think there is some thing wrong with it.
>> You said I shouldn't cap the interaction  between particles and the cylinder (3-9 LJ), but how can I do that? How can I sepperate this interaction from others during warm_up? Can you please explain  it more?
> Every LJ-interaction has its own capping parameter (see documentation of inter lennard-jones).  I'm not sure if you need to switch on this capping, by inter forcecap individual or if it just works. Please have a look at the user's guide.
> Cheers
> Stefan

JP Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609

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