Dear LAMMPS users,
I am attempting to utilize the harmonic bond potential in LAMMPS. I’m a bit confused about the meaning of the statement in the LAMMPS manual: “Note that the usual 1/2 factor is included in K.” The formula provided in the documentation is K*(r-r0)^2. The value of k in my equation (1/2k(r-r0)^2) is 2 kcal/mol/Å. Should I input 2 or half of it into LAMMPS?
You should input half of the literature value in lammps
If you have U_{bond} = K \cdot (r - r_0)^2 on one hand and U_{bond} = \frac{1}{2}k \cdot (r - r_0)^2 on the other, then straightforward calculus results in: K = \frac{1}{2}k. With k=2\frac{kcal}{mol \cdot Å} you thus get K = \frac{1}{2}\cdot k=\frac{1}{2}\cdot2\frac{kcal}{mol \cdot Å} = 1\frac{kcal}{mol \cdot Å}
how do you calculate bond coefficients? i have value of sigma and epsilon but cant figure out the way to calculate bond coefficients. i have C, H, O, Na and Cl in my system.
Please take a text book on molecular dynamics and study the chapter about classical force fields.
You can also find an abbreviated summary and lots of references in https://doi.org/10.1021/acs.jpcb.3c08419
Those would be for non-bonded Lennard Jones interactions.
For typical classical MD force fields, you don’t assign parameters by element, but by functional group. In other words, you have different sets of parameters (bonded and non-bonded) for carbon atoms depending on what functional group they are in, e.g. a CH2 in the middle of a hydrocarbon chain and a CH3 at the end, a C bound to an OH group in an alcohol, a in in a carboxylate and so on. So it is not quite clear how your parameters match your system. For a molecular system (you combination of elements suggest an aqueous solution or similar), you need LJ parameters and bond parameters and partial charges.
thank you very much, its working for me right now.