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

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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 ...
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Is there any way I can tell whether increase in total energy in molecular dynamics simulation is due to large time step or not?

Does increase due to large time step has any type of signature that will tell for certain (or almost certainly) that that is the reason?
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Why is intermolecular potential energy given in 'per mole'?

I was just wondering that if intermolecular potential is the interaction potential energy of two atoms/molecules, then why do we give its value in J/mole? I don't understand why 'per mole' ...
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Which units should I use in molecular dynamics simulation?

I have written a simple molecular dynamics simulation program. The simulation runs fine but the physical properties (in particular, I have calculated temperature) are off by many scales. I understand ...
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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 ...
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What is the potential associated to a pure torque proportional to one of the principal axis of a particle?

I'm writing a code in molecular dynamics in which a particle is subject to a pure torque around one of its principal axis. E.g., if the particle has principle axis $\hat u$, $\hat v$, $\hat f$, all ...
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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 ...
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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 ...
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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 ...
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NVT simulation of the phase transition

Why it is assumed to be incorrect to simulate,say, liquid-solid transition at constant volume (NVT simulation)?
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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 ...
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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 ...
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How introduce sound wave in molecular dynamics or dissipative dynamic particles?

How could I introduce sound wave in molecular dynamics or dissipative dynamic particles? What do specify which is applicable between molecular dynamics and dissipative particle dynamics? problem is ...
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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: $$ ...
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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 ...
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Time length molecular dynamics

What limits time length of simulation in molecular dynamics to femto and in coarse graining to nano or micro second?
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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 ...
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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 ...
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Need to Zero Angular Momentum

I'm writing a molecular dynamics simulation and need to zero the angular momentum of a collection of particles. For each particle I know the location, mass and velocity. My rotational physics is a ...
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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 ...
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Solution to a kinetic temperature problem

I have a particular equation that needs to be solved for the kinetic temperature of a stream of gas particles. If we let the kinetic temperature be designated by the letter x, the equation becomes, ...
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Applying the time evolution operator as a form of molecular dynamics

I had a kind of weird idea. In molecular dynamics, long timescale simulations (like protein folding) are a really hard problem because you can't "skip steps" of the simulation without huge ...
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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?
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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 ...
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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 ...
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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 ...
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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 ...
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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?
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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., ...
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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 ...
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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 ...
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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 ...
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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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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...