Simulating a semi-flexible long polymer chain

Dear Community Members,
I am doing a simulation of a bead spring polymer chain made of 3999 monomers. It is well known that the mean square displacement of monomer shows subdiffusive regime in the intermediate time and diffusive in the long time. But I am getting only the diffusive dynamics for all the time. I changed the parameters like timestep, total run time, damping factor. But still I am not getting the subdiffusion of monomer in intermediate time.
Could you please help me regarding this.
The input script, time-exponent plot, and log files are given in the google drive link below:

Your expertise and perspectives would be immensely valuable in identifying potential sources of discrepancy, refining simulation parameters, and interpreting the observed dynamics accurately.

I am grateful for any feedback, suggestions, or discussions you may have regarding this matter. Thank you for your time and consideration.

Best Regards

Would you like me to write the paper for you too?

Actually, I am struggling. I tried with changing parameters, but I am not getting subdiffusion in intermediate time. I don’t know where I am doing wrong. Is it possible to get some help ?

It is indeed possible, but you have to make an effort to explain to people unfamiliar with your research topic what you expected and what the simulation results are. For example, how do you distinguish between diffusive and subdiffusive regimes? I have no idea.
Also, what parameters did you change, and what is the physical rationale for those changes?

If you are trying to replicate something that is “well known”, it is often useful to try to find a paper that documents the well-known result studied with molecular dynamics and then replicate that paper, or at least compare their settings with yours.

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Basically, in diffusive regime MSD grows linearly with time and in subdiffusive regime MSD scales with time^(~1/2).
I am getting diffusive regime thoroughly which should not be.

I am still a beginner in lammps.

But it seems like your polymer is highly entangled so that the monomers form big clumps in which they can not really move freely. So except for very short time scales, the diffusion you measure is that of the clumps rather than the individual monomers. I think you should start with a much less dense starting configuration of your polymer. You may also want to start with an ideal polymer first, as the results for such an ideal polymer can be calculated analytically so you can easily see if the results are correct.

Your timestep also seems rather small to me. So you may be able to speed things up by using a larger timestep.


Thanks for your valuable suggestion :blush: . I will check it with less dense system.
I have confusion in parameters like damping factor. I want my system in over-damped condition. I choose the damping factor 0.001. Since there is no particular range of damping factor to have over-damped condition, I am a little confused. Could you please help me regarding this ? How should we choose the damping factor for the over-damped system ?

Also, when I am changing the mass value from m = 1 to m = 0.0001. then i am getting monomer’s MSD diffusive to sub-diffusive.
In literature, usually researcher take m = 1.