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

1
vote
2answers
103 views

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 ...
0
votes
2answers
184 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, ...
12
votes
1answer
252 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 ...
4
votes
1answer
779 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 ...
3
votes
1answer
237 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
51 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
136 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 ...
2
votes
1answer
182 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 ...
1
vote
1answer
100 views

What actually makes boiling happen?

Boiling can be breezed over easily with a few rudimentary diagrams and a couple equations, but I seek a deeper explanation. The definition of boiling is that the vapor pressure in the liquid is ...
1
vote
1answer
106 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
1answer
185 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 ...
1
vote
1answer
144 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 ...
0
votes
1answer
16 views

Why is the pressure value of an ideal gas for a fixed density and constant temperature of gas more than that of the same real gas?

I solved a question- Under what pressure will carbon dioxide have the density 500g/l at the temperature 300K? Carry out calculations for ideal and Van der Waals. On solving for pressure, I get For ...
0
votes
1answer
43 views

Generallized Canonical Ensemble - Isobaric Ensemble

I am trying to understand the way generalized canonical ensembles like the pressure ensemble are derived from the standard canonical ensemble. In the derivation for the standard form, one defines a ...
0
votes
1answer
14 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 ...
0
votes
1answer
68 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
89 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 ...
0
votes
1answer
43 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 ...
6
votes
0answers
561 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 ...
3
votes
0answers
34 views

Nose-Hoover Barostat

Much can be found about the Nose-Hoover Thermostat. However I seem to be having difficulty finding out details about the Nose-Hoover Barostat, and how it is implemented. Would anyone be able to give ...
2
votes
0answers
38 views

For molecular orbital, LCAO approximation is trusty?

I'm curious how the LCAO approximation is trusty. I'm majoring in physics and usually treat solid using tight binding method. Using tight binding method, We can think the periodic molecular orbital ...
2
votes
0answers
63 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
196 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
0answers
24 views

Atomic Stress (Virial Stress) and Harmonic Springs

The general context here is polymer physics. The stress tensor in a bead-spring simulation can be easily computed using the Virial Stress (which may be named the Kirkwood formula, or the Doi-Edwards ...
1
vote
0answers
19 views

Relation between solvent accessibility and brownian motion

Assume one has a molecule (made of nodes) inside a solvent. If one tries to model the average effect of the interaction between the molecule and the solvent, one has two effects: 1- Friction term on ...
1
vote
0answers
40 views

Using reflective optics concepts to focus gas pressure in a vacuum

At very low vacuum pressures the bulk behaviour of molecules can be approximated by non interacting particles bouncing off of the chamber walls: For an monotonic molecule such as He with perfect ...
1
vote
0answers
27 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
52 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
0answers
106 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 ...
1
vote
0answers
161 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
103 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
29 views

Relation between linear and rotational motion of molecules?

The temperature of a substance, such as an ideal gas, can be related to the root mean square speed of the molecules. For example, for gases the molecules travel at about 480 meters per second. If we ...
0
votes
0answers
37 views

Maxwell-Boltzmann distribution in Lennard Jones units

I'm studying thermostats in Molecular Dynamics. A very easy way (and poor, but I don't care for the moment) to implement a thermostat is to randomize momenta at some steps. These new momenta are ...
0
votes
0answers
16 views

Explicit solvent simulations in NVE ensemble: Molecular Dynamics

I am simulating a SDS micelle system in NVE ensemble at room temperature. I am not sure if the system is equilibrated, since the pressure variations are around 100's of atm, where the average pressure ...
0
votes
0answers
52 views

Calculating Microcanonical Entropy in Molecular Dynamics

As a beginning, I am simulating Argon liquid at 94 K and characterising as it is done by the Rahman's first paper on Molecular Dynamics. After going through the first two chapters of Art of Molecular ...
0
votes
0answers
18 views

Evaluation of width function; thermal neutron scattering cross section

I am attempting to perform some molecular dynamics simulation, based off of this paper, and do not have the slightest clue how they evaluate the width function (Eq. 4). My attempt at figuring it ...
0
votes
0answers
16 views

Setting up initial configuration of a Micelle - Molecular Dynamics

I have just started learning Molecular Dynamics using dl_poly_classic and analysing trajectory using nMOLDYN. Our primary aim is to do neutron scattering, but however we do Molecular Dynamics to ...
0
votes
0answers
105 views

Two Particles in a Harmonic Oscillator with repulsive short-range potential

Do bear with me, I am attempting to learn to write some simulations on the computer and learn some simple MD, so I defined sort of a toy problem. I have two particles confined in a Harmonic Potential ...
0
votes
0answers
81 views

Calculating atomic forces from total force and torque on molecule in molecular dynamics (MD)

I guess this problem applies to any body that is composed of a small number of particles, but for the sake of simplicity and concreteness, let's consider a classical model of a molecule consisting of ...
0
votes
0answers
67 views

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?
0
votes
0answers
70 views

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 ...
0
votes
0answers
105 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). My question is: How are these two fields related to ...
0
votes
0answers
164 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, ...
0
votes
0answers
41 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?
0
votes
0answers
71 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 ...
0
votes
0answers
89 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 ...
0
votes
0answers
105 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 ...