Recently I’m working on MD simulation of Polyethylene, but I encounter an problem about how to set up united atom in lammps. For example, I first generated the structure of polyethylene with chain length of 2 using Materials Studio, which is CH3-CH2-CH2-CH3. Then I convert it to lammps data file using the msi2lmp tool. But what should I do to specify CH3 and CH2 to united atom in lammps input file? Or, it should be specified in MS prior to be converted into lammps data file? Any instruction is highly appreciated!
in a united atom representation only the carbon atom location
remain. it is not lammps' job to set the force field parameters,
but your responsibility. i dont use material studio, so i cannot
tell you, if it is able to do this for you.
Polyethylene is basically a very long alkane/hydrocarbon chain, so you
could use one of the many available force field for this system, for
instance the old but still widely used OPLS model:
William L. Jorgensen, Jeffry D. Madura, and Carol J. Swenson, J. Am.
Chem. Soc. 1984, 106, 6638.