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
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 ...
2
votes
1answer
185 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
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 ...
1
vote
1answer
132 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
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 ...
3
votes
1answer
243 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 ...
1
vote
1answer
151 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
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 ...
1
vote
2answers
188 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, ...
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
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 ...
13
votes
1answer
259 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
787 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 ...
26
votes
6answers
5k 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 ...
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 ...
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 ...
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 ...
3
votes
2answers
110 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
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 ...
1
vote
1answer
435 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
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 ...
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
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 ...
4
votes
0answers
39 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
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 ...
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
0answers
108 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
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 ...
0
votes
0answers
57 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 ...
3
votes
2answers
108 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
160 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 ...
0
votes
2answers
118 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
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 ...
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 ...
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 ...
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 ...
3
votes
1answer
186 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)} ...
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 ...
0
votes
0answers
109 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
2answers
3k 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 ...
14
votes
5answers
4k 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 ...
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
86 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 ...