Re: [ESPResSo-users] Suddenly energy increases alot

[Stefan Kesselheim]

Please send us also your warmup code.

On Mar 19, 2014, at 3:40 PM, roya moghaddasi <address@hidden> wrote:

> 
> 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
> and
> 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,
> best,
> Roya
> 
> 
> 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.
> 
> 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
>> 
>> 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
> 
> 
>