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[ESPResSo-users] Error that i am unable to understand

From: yash patel
Subject: [ESPResSo-users] Error that i am unable to understand
Date: Tue, 12 Apr 2016 18:54:49 +0530

Hello All,

I hope this email finds you well. I hope you guys can help me to solve the problem that I am stuck with. I am trying to simulate a polymer with 150 monomers in a sea of obstacles (crowded environment) which are of 'type 0'. I want the polymer to be such that the first 75 monomers are of type 1 then the next 75 are of type 0. These monomers should be connected by a FENE bond.

In order to do so, I have tried to create a polymer with 75 monomers of type 1 particles and another polymer of 75 monomers of type 0 particles. i then connected them using the 'bond' command

" part 74 bond 0 75"
where 74 and 75 are the partid of last monomer of the first polymer and the first monomer of the second polymer respectively. (Can I do this?)

When I run the code I get an error like this:

Stop if minimal distance is larger than 0.9
background_errors { ERROR: bond broken between particles 74 and 75. Distance vector: -5.90274 -6.07929 6.61994 in function void add_bonded_force(Particle*) (forces_inline.hpp:903) on node 0 }
    while executing
"integrate $warm_steps"
    ("while" body line 3)
    invoked from within
"while { $i < $warm_n_times && $act_min_dist < $min_dist } {
    integrate $warm_steps

    # Visualization
    if { $vmd_output=="yes" } { imd posit..."
    (file "two_polymers.tcl" line 169)

It says that the bond between the two polymers is getting broken. Why?? Please help me out with a alternative if this is wrong.

P.S: I have attached the .tcl file with this mail just in case.

Thanks and Regards,


Yash Patel

Final Year Undergraduate, IIT Bombay

Indian Institute of Technology Bombay

109 | Hostel - 4 | IIT Bombay | Powai | Mumbai - 400 076

Mob: +91 9920168689

Attachment: two_polymers.tcl
Description: Tcl script

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