how to simulate the macromolecular organic molecules

Dear Lammps users/developers,

Now, I want to simulate the performance of particles made of macromolecular organic compounds, but I don’t know whether the LAMMPS can do this. I think the key question is how to build the “data.file” and write the force field parameters in the “in.file”, because the number of atoms is very large. Whether there is a special way to solve such problems?

Could you please give me some suggestions for this simulation?

Thank you very much for your attention!

Best regards!
Zhang

Hi,

A list of pre-post processing software is mentioned here:

http://lammps.sandia.gov/prepost.html

Hope this helps.

Usually these tools tend to be very force-field specific (and software) specific. (One reason for this is that different force-fields use different atom nomenclatures.)

Typically you would:

  1. choose the force field that you want to use, and then
  2. choose the simulation program which supports that force field the best, and then
  3. choose the best tool to build input files for that program. (For example, AmberTools is a huge and complicated program which does everything from adding missing hydrogen atoms to running quantum chemistry calculations to assign atom charge.)

People who are trying to simulate proteins and nucleic acids typically use simulation software which are specialized for running these kinds of simulations, like OpenMM, Gromacs, NAMD, AMBER. LAMMPS can simulate these kinds of molecule as well (as long as you don’t need GBSA solvent), but it requires more work from the user to prepare the input and data files.

Xiaolin Xu recommended this link:
http://lammps.sandia.gov/prepost.html

I agree that this is a good list.

However I would add that if you are willing to use the CHARMM force-field, then I would also take a look at the “chm2lmp” tool (which comes with LAMMPS). I am told it can read PDB files and also generate CMAP interactions. You are still responsible to prepare the PDB file in a way that it can understand. (I suspect a random PDB file downloaded from rcsb.org will not work. There process often requires a lot of steps.)

Andrew

(moltemplate cannot yet determine atom type from PDB files, but these other tools can.)