pair coeff

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1

Dear LAMMPS users,

I am trying to find thermal conductivity of combination of bio-molecules/crystals (mainly hydroxyapatite and collagen).

I have used topo tools to get lammps input data file from PDB file. Although I have got all the co-ordinates, angles, dihedrals, impropers etc., I am particularly finding difficulty in giving pair coefficients.
As there are 17 atom types, 1 bond type, 21 angle types, 20 dihedral types, 3 improper types, I am confused how to give pair coefficients!!
I am using LJ potential for starting purpose. Later I will go for other potentials for getting closer values to literature. If anybody have got lammps input script (apart from manual ) for predicting thermal conductivity of bio-molecules /crystals , kindly pass on as it will be much more helpful .

I am attaching the lammps input data file

molecule.txt (241 KB)

2

Dear LAMMPS users,

I am trying to find thermal conductivity of combination of bio-molecules/crystals (mainly hydroxyapatite and collagen).

I have used topo tools to get lammps input data file from PDB file. Although I have got all the co-ordinates, angles, dihedrals, impropers etc., I am particularly finding difficulty in giving pair coefficients.
As there are 17 atom types, 1 bond type, 21 angle types, 20 dihedral types, 3 improper types, I am confused how to give pair coefficients!!
I am using LJ potential for starting purpose. Later I will go for other potentials for getting closer values to literature. If anybody have got lammps input script (apart from manual ) for predicting thermal conductivity of bio-molecules /crystals , kindly pass on as it will be much more helpful .

I am attaching the lammps input data file

Thanks

Mahesh

molecule.txt (241 KB)

3

I’m confused by what you mean. If you have values for sigma and epsilon and don’t know how to specify them, it’s like this:

pair_coeff <atom type 1> <atom type 2>

You can use wildcards, so if you want atom 1 to interact with all atom types in the same way you can write:

pair_coeff 1 * …

If you want to know how to get the values for epsilon, sigma, and the cutoff, that’s really a question about your model and not about LAMMPS. You should be able to find those values in the same place that you got the diehdral and angle coefficients.