I came across parameterizing a finitely extensible model for polymers. The maximum stretch length is approximately 3.5 in sigma units. This means that the bonded interaction energy will have a maximum ...
Deriving the change in the Helmholtz free energy in the context of the free energy perturbation method
I am reading Free Energy Calculations: Theory and Applications in Chemistry and Biology by Chipot and Pohorille. At the beginning of the text (page 19, for example), the authors define the Helmholtz ...
I'm going over some (molecular dynamics) related literature - specifically the derivation of the Weighted Histogram Analysis Method (WHAM). As a quick backdrop WHAM is a method for stitching ...
I'm writing my first MD simulation (ever) for liquid Argon. The code is up and running. I am supposed to do the calculations in the NVE ensemble. Having implemented a 4th order symplectic integrator ...
Why is the canonical ($NVT$) ensemble often used for (classical) molecular dynamics (MD) simulations?
Molecular dynamics (MD) simulation is a common approach to the (classical) many-body problem. It relies on integration of Newton's equations of motion to simulate the trajectories of many (e.g., ...