Hello Dr. Kohlmey:
I have some questions about the use of “Special_bond” command in Lammps.
1- Lets say that I’m using the amber force field that scales the Coulombic and LJ weight factor automatically. Now, if I’m simulating a molecule like Acetonitrile. Does this means that all three hydrogen in the methyl group will be scaled with the nitrogen or only one will be scaled?
2- If I have a molecule with more than four atoms along their chain, does this means that the scaling is done to every four pairs locally?
3- If I’m interested in simulating a mixture of molecules that some obey this scaling factor and some that they don’t, then I should manually apply this pair interaction (scaling)?
Thanks
Shah
How and why. Whatever the amber software does is irrelevant, only what LAMMPS does matters and nobody can comment without seeing a specific example.
This question indicates that you have not fully understood how exclusions work and what the specific settings are for 1-2, 1-3, or 1-4 pairs. I suggest your revert to a text book explaining this before continuing.
See my comment above. As such this question makes no sense.
This means you would be mixing different force fields. This is a very bad idea to begin with and thus it is strongly advised against it. For some limited applications, there is a hack that can be used with pair style hybrid: pair_style hybrid command — LAMMPS documentation
Sorry if I was not specific.
The use of Amber keyword, means that automatically the following line will be executed:
special_bonds lj 0 0 0.5 coul 0 0 0.83.
This is the default for amber force field implemented by LAMMPS. I hope this clarifies the confusion.
This statement is misleading. There is no “amber force field implemented by LAMMPS”.
LAMMPS has pair styles, bond styles, angle styles, dihedral styles, improper styles, and kspace styles. If you choose the correct combination of those, you may be able to reproduce certain Amber force field versions. Same goes for the special_bonds amber command. This represents the choice for selected versions of the Amber force fields, but not all of them. Some need different scaling factors for 1-4 interactions (and this only applies to 1-4 non-bonded exclusions).
So, at best you can say that LAMMPS can represent certain versions of the Amber force field.
You may want to check out this recent discussion, for example: Protein Simulations -- Documentation Unclear
Yes, Amber is define by the choice of bond styles, angle styles and etc. For the time being lets assume I only care about 1-4 interactions that are bonded via three intermediate bonds. These are the only non-bonded interactions that I’m interested in. Also, the value of the scaling factor is irrelevant to the conversion.
Now my question is, if I have 1-4 interaction, for which the starting point is the same atom but the end is a different atoms then this scaling is done more than one time or not?
My second question, if I have more than 4 atoms in my chain, then every non-bonded atoms that are separated by three intermediate bonds will be scaled as well or not?
The scaling is done more tha one time (for all 1-4 neighbours of each and all atoms).
For what is worth it, note that the default is to find 1-4 neighbors based on the bonds section (ie how many bonds away a given atom is from one another) and not dihedral.
I don’t understand this question. You are asking if ALL atoms sitting FARTHER than three bonds away from a given one will also have their interaction scaled? If that’s the question, then obviously no. It’s only valid for 1-4 neighbors. And it’s valid for all 1-4 neighbors.
This is not really a question about LAMMPS but about how force fields work.
If you want to learn about this, you can - for example - have a look at the introduction (aka “primer”) of this recent publication, that tries to summarize molecular force fields for people that lack the molecular simulation background. https://doi.org/10.1021/acs.jpcb.3c08419
That makes it off-topic for the LAMMPS categories. You are most welcome to continue the discussion in the Science Talk category. Thus I will close this topic here now.