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Re: [ESPResSo-users] FENE+LJ bond


From: address@hidden
Subject: Re: [ESPResSo-users] FENE+LJ bond
Date: Tue, 21 May 2019 21:33:45 +0800

I tired to set different type of each particle, since the number of particles is about 40000 and the time is very long which leads me to find a new way. 
I'm appreciate for your help.

Best regards!
Ricky

address@hidden
 
From: Peter Košovan
Date: 2019-05-21 21:24
To: address@hidden
CC: address@hidden
Subject: Re: Re: [ESPResSo-users] FENE+LJ bond
I do not know how it works in LAMMPS that the authors used but in Espresso you can only set LJ or WCA between all pairs of particles of a given type. That makes good sense because short-range interactions of the same type of particles should be the same. You cannot set WCA only between pairs of polymer beads which are connected by a bond.

If you insist on it, you can set a different type to each particle of your polymer, and then explicitly set WCA for each pair of bonded particles. But that will make your script complicated with no real benefit.

Greetings,

peter

On Tue, May 21, 2019 at 3:11 PM address@hidden <address@hidden> wrote:
As the paper said,  
    "For the classical Kremer and Grest (KG) model, only a repulsive force is employed, i.e., Rc = 2^(1/6)σ. Such a model is close to an athermal model of polymer, lacking the ability to predict the glass transition driven by temperature. Furthermore, some simulation results reveal a negative thermal expansion coefficient without attraction."
Because I want to predict the Tg,  I think the cutoff should be 2.5sigma.  I think I should add the fene+lj bond on my own. Do you have some better ideas?

In addition, Do you mean that you would use WCA between all the polymer beads?

Thanks so much!

Best regards!
Ricky

 
Date: 2019-05-21 20:59
Subject: Re: [ESPResSo-users] FENE+LJ bond
Actually, they did not specify in the paper for which pairs of particles they used the usual LJ potential (Eq.1).  They only say that the fene + LJ (WCA) with cut=2^1/6 sigma) is used for polymer-polymer interactions. The text suggests that they used Eq.1 for all particle pairs including the polymer but that would be a very wierd setting.

If you need to model exactly the same system, then I think that you should ask the authors for clarification. Otherwise, I would use WCA potential for polymer-polymer and LJ with cut=2.5sigma fro all other pairs.

Greetings,

peter

On Tue, May 21, 2019 at 2:54 PM Dusan Racko <address@hidden> wrote:
Hi, isn't that a cutoff for the attractive potential to model magnetic particles only? Sorry, I don't know the papers, just suggesting

On Tue, May 21, 2019 at 2:51 PM address@hidden <address@hidden> wrote:
Dear Peter,

Actually, in the paper, the cutoff distance of LJ potential between nonbonded beads is 2.5[sigma] while the cutoff distance of LJ potential between bonded beads is 2^(1/6)[sigma]. This can't be done by your way. 
Thanks anyway!

Regards!
Ricky


 
Date: 2019-05-21 20:44
Subject: Re: [ESPResSo-users] FENE+LJ bond
Hi Ricky,

Just set up a FENE potential between the given pair of particles, and an LJ potential between the given particle types (probably the same type) and you get exactly what you want. This is the standard setup which is just described in a weird way in the paper that you cited.

The fene potential acts just between the two particles with a given id. The LJ potential acts between any pair of particles. If your pair of particles interacts both with fene and LJ, then you get the fene+LJ interaction.

See also the script  minimal-polymer.py in the samples directory.


peter

On Tue, May 21, 2019 at 10:37 AM address@hidden <address@hidden> wrote:
Dear Sebastian,

Thanks for your reply at first!
I want to model the hard-soft block copolymers with magnetic particles and the copolymer model I use is from this paper
In this paper, the bond potential is FENE+LJ.  Beyond that, I can also find paper using FENE+LJ potentials in https://aip.scitation.org/doi/10.1063/1.458541What's more, in LAMMPS, it also uses the FENE+LJ type fene bond.

I will use the FENE+LJ bond with bonded beads and the LJ potential with nonbonded beads.

Regards!
Ricky




--
Dr. Peter Košovan

Department 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

www.natur.cuni.cz/chemistry/fyzchem/
Tel. +420221951029
Fax +420224919752


--
_____________________
Polymer Institute of the Slovak Academy of Sciences
Dubravska cesta 3
845 41 Bratislava, Slovak Republic []
tel: +421 2 3229 4321


--
Dr. Peter Košovan

Department 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

www.natur.cuni.cz/chemistry/fyzchem/
Tel. +420221951029
Fax +420224919752


--
Dr. Peter Košovan

Department 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

www.natur.cuni.cz/chemistry/fyzchem/
Tel. +420221951029
Fax +420224919752

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