Regarding exclusion of intramolecular non-bonded interaction b/n monomers separated by more than 4 monomers in a 50 ru chain

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1

Dear all,

I wish to perform vacuum simulation of a 50 repeating unit chain. I want to remove the intramolecular non-bonded interaction between all the monomers of the chain which are separated by more than 4 monomers.

I wish to do this because I want to map this system to the corresponding coarse-grained (CG) representation where each monomer forms a bead, and get the corresponding bond, angle, and dihedral distribution for the CG system purely on the basis of bonded potential and no contributions from non-bonded interactions.

I try to do this by running a simulation with dummy bonds between all pairs for which I do not want to compute the non-bonded interactions. Is this correct way to do this?

Or should I perform simulation without any dummy bonds, and then use rerun command to generate
a new trajectory with all the exclusions involved?

Or is there some other way to do this?

I would be grateful for any suggestions.

Thank you.

Sanjeet

2

How is this a question about LAMMPS?

3

Dear Axel,

I am trying to do this on LAMMPS.

Thank you.

Sanjeet

4

Yes, but you are not asking about LAMMPS but rather about how to do your research.
That makes this a topic for discussion with your adviser/tutor/mentor/collaborator.
Basically you need to discuss this with people that know and care about your research.

A forum about a specific software is not the right place for that.

To make this a LAMMPS question, you would need to provide a small input and data file that demonstrates what you are currently doing, show or explain how it does or does not do what you are looking for and then ask specific questions about commands or alternatives to commands and settings etc.

5

Maybe you could use neigh_modify exclude molecule/intra all. Please check the documentation for more details.

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