[lammps-users] msi2lmp converter (LAMMPS)

Hi George,

ms2lmp is not reliable. I have also noticed this tool cannot give complete parameters for
some of my models. I think it also led to erroneous publications. The tool is still useful
if you do careful examination after generating the output. Personally I think this tool really
need to be updated or to be removed from the official release. The reason is simple, to
assign FF parameters is a critical step in a simulation. The worst case is you find your
simulation taking days or even weeks used wrong parameters.

Ting (KULeuven)

Dear Ting,

I understand your concern. It makes complete sense to cross-check the parameters otherwise it is of no use. In my opinion, the code is only automize a part of your conversion, instead of hand typing all the parameters and the coordinates. The best way, apart from visual check, is to calculate single point potential energy using MS as well as LAMMPS.

Best Regards,

Thanks, Vikas!
You confirmed what one normally has to do while using the msi2lmp tool.
It does most of the work but not complete. I can give two examples for this

  1. msi2lmp does not always output the cross-terms correctly (e.g. bondbond13 in cff)
  2. It does not handle the failsafe parameters (with ‘auto’ suffix) in FFs (e.g.cff91,cvff …)

Therefore, in order to get exactly the same single point energy as that obtained from MS, in lammps
we have to do two things:

  1. visually check the parameters already generated by msi2lmp
  2. add additional terms to some pair interactions using ‘***_style hybrid’ to include the failsafe terms.
    Or the consistency of the FFs will be broken.

One common mistake made by beginner or sometimes even by experienced modelers is
to use incomplete FF parameter set or mix parameters from different FFs. I think the former case
is much easier to get overlooked than the later one.

Ting (KULeuven)

Hi, Vikas,

It might be very naive question. But how to calculate the single point potential energy by LAMMPS?

Besides, to compare the parameters, where do I find the the required parameters base for a certain FF instead of using “.frc” files of the msi2lmp tool folder?


Hey Fei,

You could use “minimization” command can set the max value for energy and force iteraction to zero for
calculating the single point energy.

For parameters of other force fields, you could refer to relevant literature or check other simulation software like Gromacs,
Amber or Charmm which shipped with some force fields already. But you should learn the formats of them then extract
or convert the FF parameters into lammps format.

Ting (KULeuven)

Hey Fei,

You could use "minimization" command can set the max value for energy and
force iteraction to zero for
calculating the single point energy.

even better is to do a "run 0" with no integrator defined.