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Re: [ESPResSo] Self-avoiding random walk SAW


From: Axel Arnold
Subject: Re: [ESPResSo] Self-avoiding random walk SAW
Date: Mon, 2 Aug 2010 15:00:55 +0200
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On Friday 30 July 2010 19:18:14 Mikheil Azatov wrote:
> Hi,
>
> Here is a sample of the code.
>
>
> In the beginning there are some variables that I use,  so just skip that
> part because I removed parts of the code and some of the variables are not
> even used ( and some setmd commands are the ones that i added myself). I
> just wanted to send still compiling version. But basically I put 50
> polymers each having 10 monomers with parameter SAW set to 8. Then I
> calculate mindist and it's around 2.

> for {set i 0 } {$i < $npol} {incr i} {
> puts "i=$i"
> polymer 1 $npart 8 start [expr $i*$npart] pos [expr 100*[t_random]+200]
> [expr 100*[t_random]+200] [expr 100*[t_random]+200] mode SAW 8 bond 1 angle
> [expr 0.9*[PI]]

Hi!

You manually fix the first position of each polymer you add. Therefore, that 
one can overlap with the already added polymers - since you force its 
position, Espresso cannot remove overlaps with existing particles. Just don't 
specify the start position, or just from the very beginning call

polymer $npol $npart 8 mode SAW 8 bond 1 angle [expr 0.9*[PI]]

Note that depending on how dense your system is, that can take _quite_ long. 
An alternative way of generating your setup would be to use random walks, and 
slowly turning on all the interactions so that beads remove overlap by 
themselves. For the LJ potential, that is done via "setmd ljforcecap $cap", 
for the bond potentials, you can simply very slowly increase the force 
constant. This requires a bit  of tuning until it reliably works, but is 
faster than waiting for a dense melt being setup as SAWs.

Many regards,
Axel

-- 
JP Dr. Axel Arnold Tel: +49 711 685 67609
ICP, Universit├Ąt Stuttgart      Email: address@hidden
Pfaffenwaldring 27
70569 Stuttgart, Germany




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