[ESPResSo] What happens if the polymer was not built?

[Mikheil Azatov]

Hi,

I'm running the simulation in Espresso and I receive very weird results. I usually get a couple of warnings like this below but I thought it wouldn't be a problem.

Warning! Attempt #1 to build polymer 45 failed after 1000000 unsuccessful trials to place monomer 23!

         Retrying by re-setting the start-monomer of current chain...

After running the simulations I get that  some of the particles have exactly the same coordinates(looked through pdb file). So I can have one polymer kind of merging into another one but not being even close to it, so i have bonds across the whole box. After merging into another polymer the next particles of the first polymer are just copies of the other polymer with the same coordinates. This happens when the polymer hits the border of the simulation box where I have wall constraints.

I'm not sure if this is because the polymers are not built or because of the constraints but I was wondering if anyone had any idea about what I'm doing wrong.

Thank you,

Mikheil Azatov

University of Maryland

Below I have a simplified code of the simulation to make it easier to understand.

set box_l 600

setmd box_l $box_l $box_l $box_l

setmd periodic 0 0 0

set npart2 30 

set npol2 50

set kangle 257.5

inter 1 harmonic 10 8

inter 2 angle $kangle [expr [PI]]

inter 3 harmonic 10 3

constraint wall normal 0 0 -1 dist [expr -($box_l)] type 2

constraint wall normal 0 0 1 dist 0 type 2

constraint wall normal 0 -1 0 dist [expr -($box_l)] type 2

constraint wall normal 0 1 0 dist 0 type 2

constraint wall normal -1 0 0 dist [expr -($box_l)] type 2

constraint wall normal 1 0 0 dist 0 type 2

set seed "[pid]"

set seeds {}

for {set i 0} {$i < [setmd n_nodes]} {incr i} {

   lappend seeds [expr ($i+1)*$seed]

}

eval t_random seed $seeds

polymer $npol2 $npart2 8 start 0 mode RW 0 1000000 bond 1 angle [expr 0.7*[PI]] constraints

for {set i 0 } {$i < [expr $npol2] } {incr i} {

     for {set j 1} { $j < $npart2-1 } {incr j} {

     part [expr $j+$i*$npart2] bond 2 [expr $j+$i*$npart2-1] [expr $j+$i*$npart2+1]

     }

   

     for {set j 0} { $j < $npart2 } {incr j} {

     part [expr $j+$i*$npart2] mass 2.17

     part [expr $j+$i*$npart2] mol [expr $i]

     }

}

constraint delete