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
5 views

2D slab model for LJ potential

I have a program implementing a LJ(Lennard-Jones) molecular Dynamics(MD) simulation with isokinetic thermostat. I want to modify that program to study the phase characteristics of LJ particlesin 2D ...
0
votes
1answer
41 views

Notation of a vector containing equation in a paper

I'm trying to implement Coulomb long range interactions into a molecular simulation program using a particle-particle/particle-mesh Ewald solver. The following equation from the paper "How to mesh up ...
1
vote
0answers
69 views

Time Scales Of Processes In Molecular Dynamics

Suppose I run a molecular dynamics simulation of a fluid sandwiched between solid walls which are periodic in the lateral directions and finite in the direction of the fluid film thickness. Now, I ...
0
votes
0answers
19 views

How strong is the HCN Union when modelling with springs

I'm modeling the HCN Molecule with springs, giving the bounds between H and C the name k1 and between C and N k2. Is there any information of how strong is the bound? We were asked to get the ...
6
votes
1answer
80 views

FCC-to-BCC phase transition in NaCl, Buckingham or Lennard-Jones potentials?

Background The transformation from B1 (face centered cubic (FCC) type) to B2 (body centered cubic (body centered cubic (BCC) type) structures is one of the best documented high pressure phase ...
0
votes
1answer
18 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 ...
-2
votes
2answers
77 views

It's not the size of your magnet?

Growing up I've seen magnets on the fridge to the cows stomach and the latest that I know of, neodymium. On a molecular level what makes some magnetic material stronger and last longer than others?
0
votes
0answers
30 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 ...
1
vote
0answers
26 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 ...
5
votes
0answers
40 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 ...
0
votes
0answers
38 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 ...
3
votes
2answers
111 views

Gases Expanding and Bonding in the Vacuum? Frozen Clouds

Why do gasses expand in space rather than attract forming a liquid? Do some gasses attract or bond when they get colder and what would be the characteristics of it in space? Would it be like powder ...
0
votes
0answers
17 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 ...
1
vote
1answer
33 views

Thermostat in Dissipative Particle Dynamics

I'm doing a computational experiment about dynamics of a solvated line polymer, with dissipative particle dynamics(DPD). However when I try to measure kinetic temperature of the whole system(monomers ...
1
vote
0answers
20 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
1answer
135 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 ...
0
votes
0answers
59 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
1answer
44 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
2answers
119 views

Why is the trajectory of the alpha particle in a cloud chamber almost straight?

This question baffled me since high school. Presumably, the alpha particle has collided with macroscopically large number of molecules when it makes a macroscopically large displacement. One would ...
0
votes
0answers
19 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 ...
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
1answer
92 views

Why is modelling water so difficult?

There are several models of water that have come into existence so far. Nevertheless, there is no one particular model which effectively gives all the properties of water correctly. A model like TIP3P ...
0
votes
0answers
17 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 ...
26
votes
6answers
3k views

How can fast moving particles gain energy from slow moving ones?

Imagine a large diameter piston filled with water connected to a small funnel. When you press on the piston slowly but with considerable force the water will move very quickly from the funnel in form ...
3
votes
1answer
187 views

Calculation of long-range forces in Molecular Dynamics - Ewald summation

I am trying to write a code to calculate the potential and forces, for the same using ewald summation.For this purpose, the formula for potential and force I have used is : $$ U = U^{(r)} + U^{(k)} ...
3
votes
1answer
46 views

Symmetry in program for ewald summation

The formula for Ewald summation as given in Allen and Tildesley - $$ U = U^{(r)} + U^{(k)} + U^{(bc)} + U^{self} $$ where the k-space contribution of potential is given by $$ U^{(k)} = \frac{1}{\pi ...
1
vote
1answer
42 views

What is thermophoresis?

I read wikipedia article and I saw a bad youtube presentation on thermophoresis, however I don't have a clear insight about the subject. I assume the forces are basically Brownian molecular forces ...
1
vote
3answers
141 views

Langevin Equation - Stochastic Differential Equation. What are the subtleties?

I am trying to find out the motion of a particle in 3D governed by the Langevin equation, numerically. Anyway, the Langevin equation is given by $$m \ddot{x} = -(6\pi a\nu) \dot{x} + F_b $$ where ...
0
votes
0answers
110 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 ...
1
vote
1answer
82 views

Good book for learning fluid statistics

I'm currently using Gray and Gubbins Theory of Molecular Fluids to learn about the statistical physics of fluids. It may be a fine reference text, but I'm not impressed with it as an introduction to ...
0
votes
0answers
87 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 ...
-1
votes
1answer
63 views

Lennard Jones Total system energy [closed]

i am trying to implement/extend an implementation of Lennard-Jones potential simulation regarding Xenon molecules (for curious ones, the code can be found here functions (force_naive->lj_force)). ...
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 ...
0
votes
0answers
70 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?
1
vote
3answers
62 views

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' ...
1
vote
2answers
217 views

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 ...
0
votes
0answers
71 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
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
2answers
37 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 ...
1
vote
2answers
110 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
0answers
31 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
109 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 ...
1
vote
0answers
28 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
1answer
98 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 ...
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)?
1
vote
0answers
55 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 ...
2
votes
0answers
66 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: $$ ...
1
vote
1answer
110 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 ...
2
votes
1answer
185 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?
0
votes
2answers
110 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 ...