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's user avatar
  • 34.7k
9 votes
Accepted

What is the procedure to develop a new force field for molecular simulation?

The most useful answer to "how do I develop a novel force field for proteins" is "don't". (Or collaborate with a group which does.) Developing a protein force field is ...
Shern Ren Tee's user avatar
7 votes

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
7 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
6 votes
Accepted

Is the term "Forcefield" only reserved for MD (Molecular Dynamics)?

My experience is that people use the term "potential" and "force field" nearly inter-changeably. This is because the force at a particular point on a potential energy surface (i.e. ...
jheindel's user avatar
  • 3,534
5 votes

Classical MD Simulation for mineralization process

Fair Note: I have experience with only studying aggregation of small molecules at the solid - liquid interface. If you are trying to study the formation of an ordered structure from a solution phase ...
Hemanth Haridas's user avatar
4 votes

When and why are torques needed in molecular dynamics simulations?

There is a wide variety of molecular dynamics force fields; many incorporate (per-particle) torques, as you have noted, but many do not. For example, I am not familiar with any atomistic protein force ...
Shern Ren Tee's user avatar
4 votes

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
  • 1,701
3 votes

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
  • 1,126
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

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
2 votes

Training a ML forcefield on a simple bulk material

I'll do my best to answer your question because I'm also currently learning about this topic. The field generated by machine learning is indeed receiving more and more attention from everyone. However,...
Tieyuan Bian's user avatar

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