Re: [ESPResSo-users] Suddenly energy increases alot

[Stefan Kesselheim]

Hi Roya,
what are your interactions? If you have a repulsive interaction between the 
cylinder and the polymer beads, you do not want to cap that interaction, 
because it should remain active also in the warmup. I'm not sure the reflecting 
constraints are well suited for warmup. You should stick to a potential 
(possibly WCA) between cylinder and polymer beads, and make sure you cap only 
the monomer-monomer interaction. Please check the documentation of 
inter forcecap individual
to do that.
Cheers
Stefan

On Mar 19, 2014, at 3:58 PM, roya moghaddasi <address@hidden> wrote:

> My warm up code:
> # WARMUP INTEGRATION
> puts "\nWarmup:"
> 
> 
> set min_dist 0.8
> set act_min_dist [analyze mindist]
> 
> # set LJ capping
> set cap 10
> inter forcecap $cap
> 
> for {set i 0} { $act_min_dist < $min_dist } {incr i} {
>     inter forcecap $cap
>     integrate 10000
> 
>     set act_min_dist [analyze mindist]
>     puts "\tstep=$i, cap=$cap, act_min_dist = $act_min_dist"
> 
>     # Increase LJ cap
>     incr cap 10
>    # inter forcecap $cap
> }
> Thank you,
> Roya
> 
> 
> 
> On Wednesday, 19 March 2014, 18:13, Stefan Kesselheim <address@hidden> wrote:
> 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
> > 
> > 
> > 
> 
>