# Tag Info

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• 760
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### What are the more efficient, or easier, methods of handling electromagnetic interactions?

You could simplify long range interaction by reducing precision with range. Useful algorithm for it is: https://en.wikipedia.org/wiki/Barnes%E2%80%93Hut_simulation It is usually used for gravity, but ...

### elastic constants transformation/basis change P21/a -> P21/n

In order to define the matrix transforming the P21/n structure into P21/a it is imperative to know the unique axis of both space groups. For example the contracted P21/n symbol can be used for the ...
• 641

### How to calculate the exchange matrix of a bilayer magentic system?

But in order to do that I need the exchange matrix of Co-CoO system which should include the constant which represents the interaction between spins in the Co part, spins in the CoO part and a ...
• 4,298
Accepted

### How should I calculate total potential in a polymer chain?

You'll want to add up all interactions that you can, up to some appropriately chosen cutoff distance. Choose the VDW cutoff such that the total energy doesn't change much if you further increase this ...
• 760
Accepted

### Definition of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins

You simply cannot go past Allen and Tildesley's Computer Simulation of Liquids as a standard textbook on molecular dynamics. Here is a particularly illuminating diagram: As the diagram says: (italics ...
• 1,016
1 vote

### What does it mean by a "site" in the case of a CG model?

As the comments have already noted, a site in an atomistic model is the location in space at which interactions occur. The most obvious thing to do is to place all interaction sites at the atomic ...
• 3,249
1 vote

### What do we simulate with molecular simulation of proteins in the theoretical research?

As @Tyberius mentioned, you can study many different things using Molecular Dynamics simulations of proteins. My senior had studied the structure and dynamics of Intrinsically Disordered Proteins (...

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