Thermal conductivity calculation of polyethylene chain using NEMD

LAMMPS LAMMPS Beginners
1

Hi all, it’s my first time running the LAMMPS program here.

Now, I’m trying to run a NEMD simulation using Fourier’s law in the polyethylene chain.

Here is my data file (the file is the most simple model I have and I will run the main model after knowing how to run this)
PE.data (3.9 KB)

I’m using a united atom force field (UAFF)

The problem is as follow:
Can anyone tell me how to write a input (.in) file for the LAMMPS simulation?

I’ve checked the lammps homepage, but still in trouble to write a input file (such as selecting thermostat, running etc.).

If there is an example of input file which calculates thermal conductivity, it will be great to refer to it.
Please let me know.

Thank you in advance,
Andrew

2

Have you looked in the literature to see how other groups have tried to do this in MD?

3

Papers that I’ve looked for doesn’t offer a .in file script.

Is there any paper that you know?

4

You have to work on your skills in finding answers from online searches. How about starting here? 8.3.6. Calculate thermal conductivity — LAMMPS documentation That one also points to a folder in the examples (sic!) folder of LAMMPS that contains examples for how to apply the LAMMPS commands (you will still have to adjust them for your specific system and check the results for convergence etc.).

Then you probably should not start with trying to do a simulation of something that is considered an advanced topic. But rather first try to reproduce simpler to determine properties.

There is a section for the general syntax in the manual, too: 5. Commands — LAMMPS documentation

There should not be a problem in the syntax since the LAMMPS documentation is extensive. However, if you have trouble to make choices for settings, then you need to learn more about the method(s) you want to apply. It is a very bad idea to start simulations without fully understanding the underlying methodology. In simulations there are many adjustable parameters that have to be tweaked for every specific system, and learning how to do that is part of the process of learning MD. That is usually done with the help of a tutor or adviser, since it is near impossible to learn all the many details on your own and from examples alone.

That should not be a problem. The technical section of a publication should provide sufficient information to reproduce it (if the reviewers have done a good enough job, that is), and a person aiming to be a computational scientist should be capable to translate that information into a proper input file for the simulation software of their choice. Expecting a read-to-use, do-this-not-that solution for a specific software is expecting too much. If you are having trouble translating the information that is provided, then this is usually as sign that you need more training in performing such simulations and thus need to discuss with your adviser or tutor about how to acquire those skills.

5

Thank you for your reply! I’m working on with your suggestions :slight_smile: