The molecular-dynamics tag has no wiki summary.
14
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1answer
187 views
Why isn't the Gear predictor-corrector algorithm for integration of the equations of motion symplectic?
Okumura et al., J. Chem. Phys. 2007 states that the Gear predictor-corrector integration scheme, used in particular in some molecular dynamics packages for the dynamics of rigid bodies using ...
7
votes
1answer
66 views
How does one geometrically quantize the Bloch equations?
I've just now rated David Bar Moshe's post (below) as an "answer", for which appreciation and thanks are given.
Nonetheless there's more to be said, and in hopes of stimulating further posts, I've ...
5
votes
1answer
177 views
What is the “direction” of the transition dipole moment? (Understanding Eq. 9.29, Charge and Energy Transfer 3rd Ed, May & Kuhn)
For a real vector $\mathbf{r}$, the direction is given by: $\hat{\mathbf{n}}=\mathbf{r}/\left|\mathbf{r}\right|$.
The transition dipole moment is a complex vector. How do you define its direction?
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3
votes
1answer
174 views
Born-Oppenheimer separation in Dirac bra-ket notation
Most derivations I have seen of the Born-Oppenheimer approximation are made using wave-functions. To understand it better, I was trying to write a derivation using Dirac notation, but I am stuck. I am ...
2
votes
1answer
37 views
Is there a typo in this modified Lennard-Jones potential?
The standard 12-6 Lennard Jones potential is given by
$$U(r_ij) = 4\epsilon\left[ \left(\frac{\sigma_{ij}}{r_{ij}}\right)^{12} - \left(\frac{\sigma_{ij}}{r_{ij}}\right)^{6} \right]$$
where ...
2
votes
1answer
60 views
Estimate the difference between two sets of atoms
I've been working on amorphous structures derived from a crystalline one (using MD) containing $N$ atoms. I want to prove that these structures are different and to quantify their "differentness". One ...
2
votes
0answers
32 views
When is classical mechanics valid for describing motion of atoms?
In Molecular Dynamics simulations, the Newton's equation of motion is used to calculate the time evolution of system. Once, I read in an introductory text that when the thermal de Broglie wavelength ...
2
votes
0answers
42 views
Phase transition through Molecular Dynamics Studies
I am doing non-equilibrium molecular dynamics to see the phase transition of single crystal metals in extreme condition (shock compression). I am using NVE to conserve total energy, every thing going ...
1
vote
2answers
217 views
Molecular Dynamics (MD) Simulation: energy fluctuations in NVE ensemble
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 ...
1
vote
1answer
56 views
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 ...
1
vote
3answers
480 views
Franck Condon Principle and Born Oppenheimer approximation
My question here is purely fundamental. I am confused with the concept in Franck Condon (FC) principle and Born Oppenheimer (BO) approximation. The FC principle is in accordance with the BO ...
1
vote
0answers
44 views
Reaction coordinate as a function of atomic positions
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 ...
0
votes
1answer
60 views
Thermionic emission and delayed emission
I want to understand the concepts behind the thermionic emission. In thermionic emission, the energy randomization occurs and the energy may be split to electronic or roto-vibrational states. If this ...
0
votes
0answers
15 views
Molecular dynamics simulation: fluctuating dipole model implementation
I'm conducting a molecular dynamics simulation for silica. Some time ago I turned to the fluctuating dipole model, and after a much efforts I'm still having problems implementing it.
In short, all ...
0
votes
0answers
30 views
Thermionic emission, delayed emission and predissociation
In molecular photodissociation, the thermionic emission, delayed emission and predissociation are the same? otherwise, what is the difference between them?
My question is not about the solids, but I ...
