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

109
votes
3answers
9k 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?
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 ...
14
votes
1answer
433 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 ...
11
votes
4answers
2k views

Does there exist a free good molecule / atom simulation software?

I'm looking for a software or software package (for example C/C++) that can simulate a lot (say thousands at least) of molecules in action (ie. in movement or attached to say static walls). I have ...
9
votes
1answer
171 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 ...
7
votes
1answer
147 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 ...
7
votes
2answers
807 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? ...
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., ...
6
votes
0answers
375 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 ...
5
votes
2answers
670 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 ...
5
votes
1answer
404 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 ...
4
votes
1answer
271 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 ...
3
votes
1answer
142 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 ...
3
votes
1answer
125 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 ...
2
votes
1answer
56 views

Time length molecular dynamics

What limits time length of simulation in molecular dynamics to femto and in coarse graining to nano or micro second?
2
votes
1answer
158 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
105 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
26 views

How can the fictitious mass in the Car-Parrinello method reproduce the “real” dynamics?

In the Car-Parrinello method, to solve simultaneously the classical equations of motion for the atoms and the Kohn-Sham equations for the electrons, the following effective Lagrangian is used: $$ ...
2
votes
0answers
30 views

Mass scaling in molecular dynamics

I've noticed some authors scale the mass of particles in molecular dynamics simulations while leaving the force field parameters the same in order to achieve materials of different densities. Does ...
2
votes
1answer
532 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 ...
2
votes
0answers
112 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
137 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 ...
2
votes
2answers
53 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
2answers
2k 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
63 views

Is there any physical simulator precise to atomic levels and quantum effects? [duplicate]

There are tons and tons of physics simulators for classical/large scale physics. I'm interested in a simulator in which you feed an input as atoms and positions and it simulates the evolution of the ...
1
vote
1answer
129 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
2k 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
1answer
49 views

Molecular simulation applied to astrobiology

There is some research group which use molecular dynamics simulations to study the origin of life according to the hypothesis of abiogenesis? I'm just beginning to know this subject so I don't know ...
1
vote
1answer
767 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 ...
1
vote
2answers
144 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 ...
1
vote
0answers
14 views

Doubt about Hard Sphere Model

I couldn't find a proper answer about this question: if I have a gas formed by a single species (ex: biatomic gas like O2), what is the diameter $\sigma$ of the relative hard sphere model? Is it the ...
1
vote
0answers
27 views

Why is it inappropriate to calculate free energy change from end points alone?

In molecular dynamics, free energy changes are estimated using a variety of protocols to establish a path between the starting and ending states. The classic example is umbrella sampling in which a ...
1
vote
1answer
29 views

Molecular dynamics and detailed balance

In developing methods to perform Monte Carlo simulations one sufficient condition to preserve the stationarity of the target probability distribution is to impose detailed balance i.e. [Gardiner page ...
1
vote
0answers
154 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: ...
1
vote
0answers
109 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 ...
1
vote
0answers
77 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 ...
1
vote
0answers
72 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, ...
1
vote
1answer
95 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 ...
1
vote
1answer
107 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
1answer
144 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 ...
0
votes
2answers
124 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 ...
0
votes
1answer
235 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
2answers
41 views

Is there such a thing as an interaction radius for molecules?

My question is about estimating the radius of influence between two molecules; picture some mixture, comprised of water, oxygen gas (in small concentrations) and a molecule we denote $G$. In the ...
0
votes
1answer
78 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
2answers
1k 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
28 views

What exactly is cutting with a knife will look like on the atomic scale? [duplicate]

Some times I like to view the world in the microscopic scale .ie. at this level all objects any thing will be collection of atoms which we normally don't view with our naked eye. At that scale I ...
0
votes
0answers
15 views

absorption and reflection of sound on molecular level

Can someone explain the reflection and absorption of sound on the molecular level? What really is reflection? Why porous and soft material absorbs sound? What's the definition of soft in terms of ...
0
votes
0answers
26 views

Difference between molecular dynamics and direct simulation Monte Carlo

I just started studying about rarefied gases and I came across the concepts of Molecular Dynamics (MD) and Direct Simulation Monte Carlo (DSMC); so here is my question: How are these two fields ...
0
votes
1answer
39 views

NVT simulation of the phase transition

Why it is assumed to be incorrect to simulate,say, liquid-solid transition at constant volume (NVT simulation)?
0
votes
1answer
80 views

Viscosity calculation of a rarefied gas

I am studying the rotational-translational relaxation of a diatomic gas (like oxygen) using a GPU in order to accelerate the calculations; during the calculations I get the translational temperature, ...