Dear LAMMPS user,
I am using a system where a plane surface is grafted by polymers. I want to study the dynamics of tracer by varying size of the tracer. I am using hybrid bond ellipsoid atom style and Lj/cut pair style where I am varying different size by sigma in the pair coefficient. But in WCA conditions the particle go out from the polymeric environment which does not show any size effect on diffusion.
How can I vary the size of the particle and which pair style should I take for this case?
Any suggestions is highly appreciated.
Thank you in advance
There is too little information here to give a definite response, but changing the sigma parameter does change the effective radius of lennard-jones interactions.
However, it is not clear from the information you provide why you would need to use atom style ellipsoid.
As for why you are not seeing a change in behavior, there is the usual assumption that you may not have a sufficient amount of data to see a clear trend, but also this is not really a question about LAMMPS but about the science of your research and that makes it more a topic for a discussion with you advisor/supervisor/tutor/colleagues than for this mailing list which focuses on LAMMPS issues.
Thanks for your response.
Q.However, it is not clear from the information you provide why you would need to use atom style ellipsoid.
Ans- I want to make the probe self-propelled. For that purpose I take it as an Ellipsoid.
Yeah, I am seeing the change in behaviour when it is inside the polymer(i.e in the lennard-jones case), for that case I agree with you but when it go outside from the polymeric environment in the WCA case, with increase in the sigma value there is no such significant change in the behavior of diffusion.
Is this a right way to take a finite size particle(tracer) along with point particles(polymers) in a system? If we can use both the finite size and point particle in a system, then how can I change the size of the tracer and what is the most preferred pairstyle I should use?
Thanks for the explanation for using atom style ellipsoid.
As I already explained previously, the remainder of your email is about the science of your research and not LAMMPS.
You need to choose options and settings and potentials as they are required for realizing your research. That is a decision independent of what MD code you are using.
How to translate the specific requirements later into a LAMMPS input is a different story.
Thus let me repeat, to discuss your research you need to talk with people familiar with this area of research. If you want to know what other people - beyond the people you can talk to in person - prefer you can study the published literature for similar studies and learn from the model and simulation descriptions in them.
Thank you for your response.