Re: [ESPResSo-users] Suddenly energy increases alot

[Axel Arnold]

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.

Axel

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,

best,

Roya

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,

peter

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?

best,

Roya

--

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

www.natur.cuni.cz/chemistry/fyzchem/
Tel. +420221951290

Fax +420224919752

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-- 
JP Dr. Axel Arnold
ICP, Universität Stuttgart
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70569 Stuttgart, Germany
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