[Top][All Lists]

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [ESPResSo-users] Suddenly energy increases alot

From: roya moghaddasi
Subject: Re: [ESPResSo-users] Suddenly energy increases alot
Date: Wed, 19 Mar 2014 07:40:24 -0700 (PDT)

Hello dear Axel,
Thank you for your reply,
I can minimize the LJ energy between polymers by enlarging the cylinder, but I can't make lower the LJ energy between polymers and cylinder in this way. One end of my 40 polymers are on the circular ring in the middle of the cylinder which radius is equal to the cylinder's radius. My code is:

set r 26
set c [expr $box_length/2]
constraint cylinder center $c $c $c axis 0 0 1 radius $r length $box_length direction -1 type 4 penetrable 0 reflecting 1
set z $c
set mypi   3.141592653589793
set j 0
set r1 26
while {$j< 360} {
set x [expr $c+(($r1-0.001)*sin(($mypi*$j)/180))]
set y [expr $c+(($r1-0.001)*cos(($mypi*$j)/180))]
set first [expr $num_monomers_per_polymer*(($j/9))]
polymer 1 $num_monomers_per_polymer 1.0 start $first pos $x $y $z mode PSAW charge -1.0 distance 1 types 0 0 FENE 0 constraints

part $first fix 1 1 1
incr j 9
I don't know how to solve this problem. I would appreciate if you help me.
Another question is :Dose the use of SAW or PSAW for polymers help to minimize my energy?
Thank you,

On Wednesday, 19 March 2014, 0:38, Axel Arnold <address@hidden> wrote:
Hi Roya,

during the warmup, you can also monitor the closest distance between two particles via "analyze mindist". If that doesn't show any tendency to increase, the density of your system is simply too high  - which you can check also directly: everything above 1 particle per diameter^3 will not work.

Otherwise, an alternative way of constructing your system could be as follows: if I got the description of your system right, you could create the system first with almost stretched polymers in a larger cylinder, and then slowly decrease the size of this cylinder (by deleting and recreating the constraint). The change must be really small, like 0.01 diameters every 100 time steps or so.


On 18.03.14 18:29, roya moghaddasi wrote:
Dear peter,
Thank you for your answer, I have a question, what do you mean by different warm_up procedure, can you introduce me a source to read more about it and about different method to generate initial state, as well.
Thank you,

On Tuesday, 18 March 2014, 20:50, Peter Košovan <address@hidden> wrote:
Dear Roya,

one possible answer is: simply make your warmup longer. You need to increase the capping gradually until all overlaps settle down to reasonable values. Then your energy should be of a comparable order of magnitude with the number of particles. Your polymers are rather long, so the warmup may take long as well. How quickly it evolves depends on your initial state and on the polymer length.

You could also consider a different warmup procedure, or a more different method to generate your initial state, such that you avoid overlaps.

With regards,


2014-03-18 18:09 GMT+01:00 roya moghaddasi <address@hidden>:
Hello every body,
In my system, there is a cylinder constraint, I assumed a circular ring in the middle of this cylinder, then I put one end of 40 polyelectrolytes on this ring (their distances are equal between each two end of the nearest polymers in the ring), the radius of this ring is 25 and the length of each polymer is 100, the problem is that suddenly the energy of the system extraordinary increases (8e40) and it is mostly because of the lj interactions between polyelectrolytes with each other and between polyelectrolytes and the constraint, after warm_up this energy decreases to(5.7e27), but it is still very high and makes my simulation unphysical, I don't know how to control this high energy and make it lower.
I would appreciate if anyone can help me?

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

Pokud je tento e-mail součástí obchodního jednání, Přírodovědecká fakulta Univerzity Karlovy v Praze:
a) si vyhrazuje právo jednání kdykoliv ukončit a to i bez uvedení důvodu,
b) stanovuje, že smlouva musí mít písemnou formu,
c) vylučuje přijetí nabídky s dodatkem či odchylkou,
d) stanovuje, že smlouva je uzavřena teprve výslovným dosažením shody na všech náležitostech smlouvy.

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

reply via email to

[Prev in Thread] Current Thread [Next in Thread]