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10 votes

Why are Coulomb interactions modeled with just r, not r squared?

The force $F$ is proportional to $\frac{1}{r^2}$ but the potential $V$ is proportional to $\frac{1}{r}$. This is because $F$ is proportional to $\frac{\partial V}{\partial r}$, the derivative of $V$ ...
Nike Dattani - No Free Time's user avatar
8 votes

Effect of temperature on Forcefield parameters in classical molecular dynamics simulations

The answer to how much information are we losing by considering a temperature-independent forcefield in such systems? is, to a first approximation, none. The reason is that the statement ...
Shern Ren Tee's user avatar
7 votes
Accepted

Effect of temperature on Forcefield parameters in classical molecular dynamics simulations

I have reasonable experience with the parameterization and MD simulations of molecules with CHARMM FF, which is one of the temperature-agnostic FF. I will try to answer the questions, but please note ...
Hemanth Haridas's user avatar
5 votes
Accepted

Force fields for generating **Co3O4 and Fe3O4 structures in LAMMPS

I am afraid your project to develop a new force field will not work from LAMMPS. The main reason is that, LAMMPS is, in simplest terms, not a first-principles simulation engine, but a molecular ...
Andrey Poletayev's user avatar
4 votes
Accepted

Advantages/Disadvantages of Qeq over Drude polarizable model?

The three main polarization models are Qeq, Drude and induced dipole. The Qeq is a charge-polarization, while the other two are dipole-polarizations. The Drude and ID are essentially equivalent, and ...
Frank Jensen's user avatar
  • 1,806
3 votes
Accepted

How to write the REBO force field

If I remember correctly, the CHO extension of the REBO force field (which was further updated in a later publication) also introduces some changes in formalism, which in turn are not implemented in ...
Kristof Bal's user avatar
  • 1,371
3 votes
Accepted

How to pre-optimize metal-organic complexes in RDKit using UFF?

Okay, there's a bunch to answer here, but I'll do my best. Take a look at the page for Tetraamminecopper(2+) sulfate on pubchem. The SMILES on there is incorrect and no geometry can be generated on ...
Geoff Hutchison's user avatar
2 votes

Forcefield parameterization techniques

There are many FFs that are available at your disposal, such as CHARMM, AMBER and OPLS. These FFs will have residues that form the part of the protein that you are interested in, and can be directly ...
Hemanth Haridas's user avatar
2 votes

Include Li+ in force field for Molecular Dynamics

So far, I could find these three sources for parameters for a LJ parametrisation of Li Ref epsilon (kJ/mol) sigma (Ang) 1 CL&P for ionic liquids 0.07648 2.126 2 Wu & Wick Macrom. 2010 1....
Marco Di Gennaro's user avatar

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