Input files for membrane simulation

Dear All,

I wish to learn LAMMPS, aimed at simulating biomolecules. I just installed it and would like to simulate a lipid membrane using the Martini forcefield.

I would be very grateful if you could provide me input files (coordinates and parameters) of any membrane system such that I can play with? Thank you very much in advance.

Best regards

For typical biomolecular simulations, I’d personally recommend GROMACS instead. It has far fewer capabilities … but that’s the point, since many LAMMPS methods are more relevant to materials science. GROMACS can often be simpler to use and faster to run, and there is a wide range of how-tos available online, including for membrane simulation.

Thank you very much for suggestions. I have used gromacs, but I find that lammps has many interesting features so I would like to learn lammps also. Have you run membrane simulation with lammps?

It’s not different from a usual LAMMPS system – you need to prepare the initial topology (Moltemplate would work well), coordinates (Packmol or the CHARMM online membrane builder), and force field parameters (from the MARTINI references – note you must manually specify “mixed” parameters, i.e. the ij coefficients). Then it should all just work!

@Phuong_Nguyen

If it is of any use, I can share a random input file for running MD for ZIF-8 (a MOF) in the CG level using a MARTINI model (version 3).
In this mapping, the Zn2+ cation is bead type 1 and the ligand (methyl-imidazole -) is bead type 2. The bead flavors within MARTINI 3 used in this script are SP5q for beads type 1 and RN2aq for beads type 2.

Ofc you would need to look in LAMMPS manual the meaning of the commands as well as adapt it for whatever it is you want to do. I dont have any sort of membrane .dat file or anything but maybe you can find that elsewhere and replace accordingly.

in.martini (1.2 KB)
pos.dat (98.2 KB)

1 Like