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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 07:36:01 -0700 (PDT)

Dear Peter,
Thank you for your answer,
but I can't have a distance between my cylinder and the first particles, It ruins my simulation, Is there any other way not to have too much energy without putting  a distance between cylinder and particles?
Thank you,

On Friday, 21 March 2014, 17:57, Peter Košovan <address@hidden> wrote:
Dear Roya,

I guess that it means that your first particle is too close to the cylinder.

In general: if you put two things too close together and assign a divergent repulsive interaction between them, you get a high energy. To get a lower energy, you need to either change the distance, or the interaction parameters. You need to insert all particles such that they do not overlap with any other particle with which they have a repulsive interaction.

What about placing your first particle 1sigma aside from the exact location of the cylinder? Will that spoil your simulation? Alternatively, you can assign a different type to it, and make sure that there is no repulsive interaction between this particle and the cylinder.

If you are placing your particles one by one, using "part pos ...", then it's a good idea to immediately check for overlaps. If the energy is too high, you need to place it elsewhere.

In the scripts directory of Espresso, there is a polymer.tcl file, which contains the tcl implementations of the polymer command and several others. You may have a look at it to get some inspiration on how to place particles to avoid overlaps.



2014-03-21 14:51 GMT+01:00 roya moghaddasi <address@hidden>:
Hi dear Axel,
I set up my polyelectrolytes as you said and the LJ energy between them become reasonable (10^3, at first it was 10^13), but there is too much energy between polyelectrolytes and the cylinder because the first particle of each polymer is sticked to the cylinder(it should be), what should I do to solve this problem?
Thank you,

On Friday, 21 March 2014, 15:55, Axel Arnold <address@hidden> wrote:
On 21.03.14 13:18, roya moghaddasi wrote:
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?

Make that a loop and place the particles manually, using "part pos".

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?

No, since if you put the rods such that there is no overlap, then there is no interaction at the beginning that could be out of range.


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

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

Dr. Peter Košovan

Departmtent of Physical and Macromolecular Chemistry
Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie
Přírodovědecká fakulta Univerzity Karlovy v Praze
Tel. +420221951290
Fax +420224919752

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