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

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How to explain the momentum exchange of two solid particles collision at molecular scale?

Here is my question: assume two solid sphere collided to each other in vacuum, at macroscopic, it can be explain by Newton's law. But at molecular scale, does the surface atoms touch to each other or ...
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182 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 ...
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154 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 ...
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41 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 ...
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603 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 ...
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143 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 ...
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44 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 ...
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157 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 ...
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109 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 ...
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114 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 ...
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10 views

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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12 views

What happens to the velocity map image if the plane of polarization is not on the plane of the detector?

In an electron Velocity Map Imaging (in Velocity Map Imaging in general) it is required that the plane of polarization to be parallel to the plane of the detector (in other words, plane or ...
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46 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)?
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95 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, ...
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54 views

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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35 views

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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419 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 ...
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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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128 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 ...
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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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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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202 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: ...
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121 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 ...
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82 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 ...
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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, ...
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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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Incoherent Intermediate Scattering Function from Molecular Dynamics Simulations

I want to calculate the incoherent intermediate scattering function (ISF) using the self-part of the van Hove function. When I plot the ISF as a function of time, should I consider the modulus of the ...
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33 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 ...
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53 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 ...
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how to find the frequency in a auto correlation function?

I am running some molecular dynamics simulation with carbon nano tubes and calculating the velocity auto-correlation function (VACF). Each 10 time steps is writen in a file the VACF and in the final ...
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45 views

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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16 views

What is the temperature effect on trajectories in phase space in molecular dynamics?

In molecular dynamics simulations or microcanonical ensemble (fixed-energy), what is the effect of temperature on the trajectories of the reacting systems (let's say two reactants react to form two ...
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Pressure components in a film

I am performing molecular-dynamics simulations of a polymer near a crystalline substrate (polymer film). I am comparing the mechanical properties in the film with the properties in the bulk polymer. ...
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29 views

Tersoff parameters

I am studying the tersoff potential i am trying to understand the physical meaning for each parameters in this potential. The development of Tersoff potential is a little fuzzy (several articles). ...
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101 views

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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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 ...
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30 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?
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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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75 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 ...
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97 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 ...