Polymer chain is breaking apart into small fragments after simulation

[Suman Das]

Dear hoomd users,

I am simulating  polymer chains of the type [A]*25 + [B]*25. I have used Lennard-Jones interactions among the particles. Also, I have used harmonic force constant of value 75000 which is similar to constrained bonds in TraPPE force field. However, I found that some polymer chains are breaking apart into small fragments after a short simulation run. Could somebody help me to figure out is there anything wrong with the input parameters? I have attached the input script and configuration file.

with regards,

Suman

[Tim Moore]

Suman,

The chains are not breaking apart. I suspect you're just seeing the effect of the periodic boundary conditions. If you're using VMD to visualize, you can unwrap the chains with "pbc join connected."

Tim

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Tim Moore

[Suman Das]

Hi Tim,

Many thanks for reply. You were right. After giving the command in VMD, I found all the polymer chains intact. I have another query. In my system I have particle type A and particle type B. I want to assign electrostatic charge (-1 for A and +1 for B) to these particle. How can I do it? Thanks again for your reply.

Regrads,

Suman 

On Sunday, June 11, 2017 at 1:42:46 PM UTC-4, Tim Moore wrote:

Suman,

The chains are not breaking apart. I suspect you're just seeing the effect of the periodic boundary conditions. If you're using VMD to visualize, you can unwrap the chains with "pbc join connected."

Tim

On Sat, Jun 10, 2017 at 9:40 PM, Suman Das <suman...@gmail.com> wrote:

Dear hoomd users,

I am simulating  polymer chains of the type [A]*25 + [B]*25. I have used Lennard-Jones interactions among the particles. Also, I have used harmonic force constant of value 75000 which is similar to constrained bonds in TraPPE force field. However, I found that some polymer chains are breaking apart into small fragments after a short simulation run. Could somebody help me to figure out is there anything wrong with the input parameters? I have attached the input script and configuration file.

with regards,

Suman

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Tim Moore

[Tim Moore]

You can modify your script to look something like this.

Tim

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Tim Moore

[Suman Das]

Hi Tim,

Many thanks for your kind reply.

Regards,

Suman