Molecular dynamics (MD) is an approach used for simulating dynamic processes through successive integration of Newton's equations of motion.

learn more… | top users | synonyms

0
votes
0answers
12 views

need some references in molecular dynamics simulation

I Just start we a new model on my project and I will need to work with Molecular dynamic simulation. I have to simulate dynamics of many filament inside a network (actomyosin network).The problem is ...
95
votes
3answers
7k views

How does a knife cut things at the atomic level?

As the title says. It is common sense that sharp things cut, but how do they work at the atomical level?
0
votes
1answer
50 views

Fock matrix elements for RHF formalism

Here I refer to a particular book Molecular Quantum Mechanics by Peter W. Atkins and Ronald S. Friedman, but similar derivation could be found in many other texts. So, when obtaining the explicit ...
0
votes
0answers
23 views

Verlet timestep

I am using velocity Verlet in molecular dynamics. Is just a simple question, if a simulation using time-step femtosecond, in velocity Verlet is just necessary $dt = 10^{-15}$ to use femtosecond?
1
vote
1answer
165 views

Understanding the mean square displacement in molecular dynamics

In a Molecular Dynamics (MD) simulation, the mean square displacement $\text{MSD}$ is given by $$\text{MSD}(\delta t) = \left\langle\left|\vec{r}(\delta t)-\vec{r}(0)\right|^2\right\rangle,$$ where ...
0
votes
0answers
12 views

Modelling of nuclear motions (Classification) after invoking the BO approximation

I know that after invoking the Born-Oppenheimer approximation, the nuclei will move on the adiabatic potential provided by the electronic energy (also called potential energy surface (PES)). Such ...
1
vote
0answers
75 views

Coherent Intermediate Scattering Function from Simulations

I want to calculate the coherent intermediate scattering function, $S_{\text{coh}} (\mathbf{Q},t)$, from a molecular dynamics trajectory, based on its definition. The definition of the function is: ...
0
votes
2answers
74 views

Molecular mean free path probability

Let's let $p(\xi)$ be the probability a molecule travels at least $\xi$ between collisions, lets say $\xi=0.01$. When I think of this statement, I think it it is the probability the molecule is able ...
17
votes
5answers
3k views

When I stretch a rubber band, it breaks. When I hold the broken ends together, why doesn't it join again?

The question is simple. When we join the two broken surfaces, what is it that keeps the surfaces from connecting with each other, while earlier they were attached to each other? Also, would the two ...
1
vote
0answers
99 views

Correct way to include constant external force in virial and pressure calculation

Halo, given a simulation cell with N particles where particles interact only with bond and pair potentials and periodic boundary conditions (minimum image convention) are used. On a subgroup of ...
0
votes
0answers
44 views

Langevin equation

A molecule consists of two atoms whose centers are located at $\mathbf{r}_1$ and $\mathbf{r}_2$ respectively. The atoms are connected by a bond that can be approximated by a harmonic spring, so that ...
0
votes
0answers
36 views

Difficult to visualize Franck-Condon overlap

The franc condon principle says about the vertical transitions, means the coordinates of the nuclei remains unchanged during an electronic transition. But, what is the physical meaning or how to ...
2
votes
2answers
44 views

Do molecular bounded systems shield or reduce neutron cross-sections?

When talking about neutron cross-sections, literature is usually investigating isolated cases of Neutron + Atom. Here, the abundance of hydrogen is dominating neutron fluxes through material. I ...
1
vote
1answer
133 views

Molecular rotation - Energy levels for an asymmetric molecule

For a molecule with spherical symmetry, the energy level of rotation for quantum number $J$ is: $$E(J)=\frac{J(J+1)\hbar^2}{8\pi^{2}I}$$ "$I$" is the Moment of inertia for the molecule ...
4
votes
1answer
161 views

Molecular dynamics: Thermostat via damping modulation

Molecular dynamics (MD) often use a thermostat so that they can control the temperature. Temperature tends to drift due to endo/exothermic reactions (that would normally absorb/emit heat to a large ...
2
votes
1answer
416 views

Moment of inertia of rotating particles in center of mass frame?

I am trying to simulate a collision between two molecules. I know the energy for every position/orientation, from which I can calculate the forces. The treatment is classical and the molecules are ...
1
vote
0answers
64 views

Any quadrupole approximation? Any example?

In atomic and molecular physics we quite often encounter with electric dipole approximation. The dipole approximation we do when the wave-length of the type of electromagnetic radiation which induces, ...
3
votes
1answer
91 views

Force field for Calcium ions, potassium ions and water in molecular dynamics

I want to adapt my existing MD simulation so that it can handle these three species. For the interactions of the ions I thought that I would use the coulomb potential, but I don't know what sort of ...
0
votes
0answers
54 views

Can peridynamics give accurate quantitative results?

I'm applying for a position that is interested in studying crack growth using peridynamics. I have experience with MD on polymeric systems, but I had never knew of this method before. It seems very ...
6
votes
0answers
273 views

Surface tension between water (liquid) methane (gas)

In my project I should calculate surface tension between water and methane with lammps. I write the program.I use SPC model for water and $l_j$ for methane and water - methane. But now I don't know ...
0
votes
2answers
883 views

Does the Lennard-Jones force equation give its answer in Newtons?

I'm trying to do the dimensional analysis of the Lennard-Jones force to work out what units are being used in my MD simulation. The lennard Jones force is given as the negative derivative of the ...
0
votes
0answers
67 views

reactions in molecular dynamics simulations

EDIT: Apparently this is called reactive molecular dynamics. It seems that the ReaxFF potential function is used for some reactions like this. I am interested in adding support for reactions to a ...
9
votes
1answer
147 views

Do Franck-Condon oscillations have natural lineshapes?

I recently found a paper (for the curious, this one) that talks about observing the motion of a nuclear wavepacket in H2O, as initiated by tunnel ionization. This wavepacket should be thought of as a ...
0
votes
0answers
64 views

What is the physical property of metal nanoparticles?

I am a Math student but now I have to deal with gold nanoparticles in aqueous solution. Now I was wondering whether the physical properties of gold nanoparticles are the same as the properties of gold ...
5
votes
2answers
469 views

Deuterium density in seawater

I heard today that deuterium for nuclear fusion could be extracted from the Oceans, in which it is present in "heavy water." I heard this claim: "Deuterium is distributed uniformly with Ocean ...
1
vote
2answers
121 views

Molecular Hamiltonian

I was reading some material on the Molecular Hamiltonian on Wiki. It said that, Almost all calculations of molecular wavefunctions are based on the separation of the Coulomb Hamiltonian first ...
0
votes
0answers
83 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 much effort I'm still having problems implementing it. In short, all ...
2
votes
1answer
127 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 ...
1
vote
1answer
119 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 ...
3
votes
1answer
130 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 ...
7
votes
2answers
629 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? ...
2
votes
1answer
104 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 ...
1
vote
1answer
93 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 ...
1
vote
3answers
1k 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 ...
2
votes
0answers
90 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 ...
2
votes
1answer
134 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
200 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 ...
1
vote
2answers
1k 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 ...
4
votes
1answer
331 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 ...
6
votes
4answers
3k views

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., ...
7
votes
1answer
129 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 ...
14
votes
1answer
359 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 ...