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Questions tagged [molecular-dynamics]

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

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Is simple sound transmission in matter normally 100% efficient or is there "leakage" to heat even when there is no damage or destruction of medium

Specifically I was wondering for instance in a perfect gas or real gas or water or steel does the medium absorb some sound as perhaps thermal energy, or can it always travel without losses through the ...
Bryan Major's user avatar
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Calculate number of air particles going through a hole in high vacuum at molecular flow

I have a vacuum chamber, connected to a vacuum pump with a pipe of diameter 50mm and need to create a high (0.0001mBar) vacuum. I need to calculate the total suction time, and since I was not in the ...
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What is the relationship between persistence length and timescale?

I have calculated the bending persistence length of a polymer using MD simulations in the nanosecond timescale. The persistence length is long (410 nm) compared to the contour length (40-45 nm). But ...
yippee's user avatar
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Intuition about SCAN-DFT

I am currently performing molecular dynamics simulations of water/ice and would like some intuition behind some of the results I am seeing. For context, I am using the water model described in this ...
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3 answers
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Does compressing air increase the average speed of the air molecules?

If you have a cubic foot of air and compress it, will the speed of the molecules stay the same or increase? I know that the air will heat up the surrounding objects because the molecules are in a more ...
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Green Kubo Relation for viscosity

I am calculating viscosity of WCA fluid using the Green Kubo relation. I am also following the paper of Zhang et al. for the Time decomposition method https://doi.org/10.1021/acs.jctc.5b00351 where, ...
Lifelong Learner's user avatar
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9 answers
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Is there such a thing as a "physical" fractal?

The recent discovery of a molecule that mimics the Sierpinski gasket has spurred headlines identifying it as the first fractal scientists have found in nature. I find these claims highly dubious ...
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How fast does information travel through air molecules?

You're always told that information travels through air (speed of sound) at appx. 767 mph. This doesn't tell you how fast the transfer of momentum happens between the actual molecules of air. So how ...
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How to deal with temperature drift when computing thermal conductivity with molecular dynamics?

Background In the $NVE$ ensemble, thermal conductivity, $\lambda_T$, can be computed from molecular dynamics (MD) using the Green-Kubo relation (Allen and Tildesley) $$\lambda_T = \frac{V}{k_B T^2} \...
Gigawatt's user avatar
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Energy distribution of water molecules without considering the free gas hypothesis

considering water molecules as a free gas at a certain temperature, their kinetic energy distribution is given by the Maxwell-Boltzmann distribution (associated with temperature), right? So, if I want ...
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Molecular stretching oscillations directions

Molecular stretching oscillations directions. If we say that vertical oscillation is up/down. Then, left/right and front/back are horizontal oscillations. Hence, when we measure oscillations of ...
Niss Green's user avatar
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Can latent heat exist when both phases cannot exist at same temperature?

This is my understanding (please tell me if i am going wrong anywhere): During phase change (i.e. ice melting into water) the molecules absorb heat, gain more random kinetic energy, and spread apart (...
Varshil MVH Pets's user avatar
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Intertial finite-size effects in fluid simulations

A gradient $\nabla \rho$ in the density field $\rho$ of fluids at thermodynamic equilibrium is suppressed at a rate given by $D \nabla^{2} \rho$, allowing to measure the diffusivity $D$ of the fluid ...
YoussefMabrouk's user avatar
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Periodic boundary conditions: torus or infinite images?

I have a "philosophical" question regarding the use of periodic boundary conditions (PBD) in modeling and simulating systems of particles. Let us consider a system of $N$ classical particles ...
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Relation between Mean Squared Displacement and Velocity Autocorrelation Function [closed]

I'm trying to understand the relation between the Mean Squared Displacement in a sample of moving atoms (for example) and the autocorrelation function of the velocity. So I read in "Understanding ...
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Calculating enthalpy of a solid as a function of temperature in Molecular Dynamics

I would like to get the enthalpy as a function of temperature for BCC lithium at zero pressure. I have performed a series of NVT simulations with 500 atoms using a Nose-Hoover thermostat at the ...
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Can free energy be computed in Molecular Dynamics (MD) by placing an aptamer close to a protein and seeing how well they dock?

There are many different ways aptamers can bind to proteins. In other words, there are multiple bound complex configurations. To test the binding affinity (free energy) of each configuration, is it ...
unit vector's user avatar
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How to tell whether Hamiltonian has rotational invariance? Conservation of angular momentum?

If a system contains isotropic exchange interaction and uniaxial anisotropy in the $z$-direction, does this Hamiltonian satisfy rotational invariance of the $z$-direction so that the spin angular ...
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Can magnetic-molecular dynamics be used to study the macroscopic rotation of a lattice? Such as the Einstein-De Haas effect and the Barnett effect

When applying molecular dynamics, it is generally assumed that the equilibrium positions of the atoms are fixed, in which case the calculated displacements of the atoms are the displacements with ...
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How do you accelerate a molecular structure with EM wave pulses without heating it up?

vibrating the atom good| heat bad|fast-moving vehicle bad| one-meter cube with different atoms trying to accelerate its whole molecular structure with EM wave pulses but not cause heating damage
ElyasThe Cool's user avatar
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Free energy as a function of temperature over phase transition in molecular dynamics simulation

I've constructed a low density standard MD simulation (in Python), using the Lennard-Jones potential with an Andersen thermostat, of 10 particles in a box V = 10 $\times$ 10 $ \times$ 10 in the NVT ...
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Regarding Degrees of Freedom and dynamics of polyatomic molecules [closed]

Justify how a molecule with N atoms have $3N-5$ vibrational degrees of freedom(Linear) and $3N-6$ vibrational degrees of freedom (Non-linear). Will this be valid for large number of N? Taking $H_2O$ ...
Aditya Krishna Panickar's user avatar
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How can I simulate multiple layers of atoms forming Turing patterns?

This experiment blew my mind -- they created a Turing pattern in a single atomic layer of bismuth adsorbed on crystalline niobium selenide. https://www.chemistryworld.com/news/tiniest-turing-patterns-...
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Diffusive finite-size effects of fluids in periodic boundary conditions

Consider a fluid of given density $\rho [\frac{kg}{cm^{3}}]$ in thermal equilibrium at a given temperature $T [K]$. If at time $t_{0}$ we apply a force $f(\vec{r}, t) = f_{0}\delta(t-t_{0})\delta(\vec{...
YoussefMabrouk's user avatar
5 votes
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Acoustic finite-size effects of simulated fluids under periodic boundary conditions

Consider a fluid simulated in a finite box of specific size. An impulse to the fluid element at the center in a given direction is physically expected to propagate at the speed of sound and attenuate ...
YoussefMabrouk's user avatar
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Systematic drift in total energy in MD simulation

I have been simulating a system of 10 particles interacting among themselves via Yukawa potential using Molecular Dynamics technique. In addition to the Yukawa interaction, there is an exterally ...
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How do you determine the Pull Direction for a GROMACS umbrella sampling simulation to generate the most accurate free energy value?

I am trying to calculate the free energy between a protein and aptamer using GROMACS. Literature has indicated that one of the best way to do so is by performing an umbrella sampling MD simulation ...
unit vector's user avatar
1 vote
1 answer
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Two-body correlation function computation [closed]

TL;DR Summary: How to compute correlation function from MD data? I'm studying how to compute excess entropy in molecular dynamics (MD). I've found it is needed to compute the two-body correlation ...
MPEI_stud's user avatar
1 vote
2 answers
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Questions regarding a derivation in Understanding Molecular Simulation: From Algorithms to Applications, 3rd ed, pp 141-143

Recently, I've been learning molecular dynamics using the third edition of the book, Understanding molecular simulation: from algorithms to applications. During reading your book, I have encountered ...
Izzy Tse's user avatar
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Does collisions of ideal gas molecules effect its equation of state?

I have been reading Statistical Mechanics by R. K. Pathria & Paul D. Beale , 4th edition . In this book they used a quantity called Virial , which is defined as $\mathcal{V} = \langle\Sigma q_iF_i\...
black photon's user avatar
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Convergence of the bias potential in well-tempered metadynamics

I have trouble understanding how the bias potential $V(s,t)$ in well-tempered metadynamics is related to the free-energy $F(s)$ by a simple relation as $t\rightarrow\infty$. Around equation 4 in the ...
Lukas's user avatar
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Autocorrelation functions - haven ratio

I'm studying Haven coefficients (I created similar question but with MSD). Right now I have question referring to calculating haven ratio using velocity-velocity autocorrelation functions. What I have ...
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Calculating cross terms for Haven coefficient using windowed MSD

My problem is that from this site: MSD Module I'm taking an equation that expresses the windowed mean squared displacement (MSD): $$MSD(m) = \frac{1}{N}\sum_{i=1}^{N}\frac{1}{N-m}\sum_{k=0}^{N-m-1}(\...
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Calculating charge diffusion coefficient from Green Kubo relation

I'm trying to calculate Haven coefficient in some crystal that I have assembled coordinates of N ions of oxygen in k time steps. I looked up equations in this article: Pressure-Dependent Diffusion ...
daryldxn's user avatar
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How to calculate windowed mean squared displacement for multiple particles?

I'm new to molecular dynamics and I find this equation pretty confusing: $MSD(\tau)=<r(t+\tau)-r(t)>$ For example take a structure with N mobile ions (e.g. oxygen particles). In different ...
daryldxn's user avatar
1 vote
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What are the $x$, $y$, and $z$ components of a force acting on $i$-th atom in a Lennard-Jones system of $N$ atoms?

What are the $x$, $y$, and $z$ components of a force acting on the i-th atom in a Lennard-Jones system of $N$ atoms? According to my understanding: The Lennard-Jones potential function is given by the ...
user avatar
3 votes
1 answer
113 views

Derivation of Pressure Correction Term in Lennard-Jones Fluid Simulation

Context Hey everyone, I'm working on a molecular dynamics assignment where I'm simulating a Lennard-Jones fluid in the Gibbs ensemble. The potential is given by equation (1): $$ U(r) = 4\epsilon \...
Kevin's user avatar
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Why fibers go to the liquid/liquid interface instead of staying in the bulk phase?

I have an ionic liquid solution phase and an organic phase. They are immiscible. When I place a small piece of nylon fibre in the liquid it always goes to the liquid/liquid interface instead of ...
Kavindu Lochana's user avatar
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Visualize sound propagation in molecular dynamics?

I am simulating a simple Lennard-Jones fluid confined between two fixed walls and I am analyzing the autocorrelation function of the velocity along the direction of the confinement (normal to the ...
YoussefMabrouk's user avatar
1 vote
0 answers
155 views

Determination of Intermediate Scattering Function in numerical simulation

The Fourier transform of single particle density : $$\rho(\textbf{k},t)=\int\rho(\textbf r,t)\exp(-i\textbf k.\textbf r)d\textbf r=\sum_j \exp(-i\textbf k.\textbf r(t))$$ The Intermediate Scattering ...
bubucodex's user avatar
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1 answer
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Normal Force - What if I stepped on a molecularly frozen object? [closed]

I’ve been trying to understand normal force on a molecular level, and I’ve come across the idea that atoms are connected to each other by forces that act like springs. You step on the floor; the floor ...
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Berry connection in condensed matter vs. molecular dynamics

In principle, a connection is totally arbitrary. Berry connection is not the connection, but rather it is simply a connection that is physically motivated. That is, mathematically, we could connect ...
Adrian Scheppe's user avatar
3 votes
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Conserved quantities in overdamped dynamics

I have an implementation of over-damped Brownian dynamics, with particles that follow the version of the Newtons law where the inertia is absent. This is a common thing to do at micrometer scale. $m x'...
user13831679's user avatar
1 vote
0 answers
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Calculating Fourier spectra of particle current autocorrelation functions

The particle current density can be defined as : $$\textbf j(\textbf r,t)=\sum_{i=1}^{N} \textbf v_i\delta(\textbf r-\textbf r_i(t))$$ Its spatial Fourier transform : $$\textbf j(\textbf k,t)=\sum_{i=...
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Radial distribution function in a plane

I have a three-dimensional system of N particles. The particle positions are described by three coordinates $x$, $y$, $z$. For this system, I can calculate the Radial Distribution Function (RDF) in 3D....
bubucodex's user avatar
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How to get temperature from the results of WHAM?

I ran a series of replica exchange molecular dynmaics for the different temperatures. I used WHAM to sample metastable states. From the results of WHAM, we can get probabilties ($p$) from the energy ...
이영규's user avatar
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1 answer
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Verlet algorithm without initial conditions

I was working on a problem asking 'in an oscillation of a bond in a single O2 molecule with a pair-wise Lennard-Jones (LJ) potential how does the total energy $E$ vs $t$ change?' it goes on to provide ...
Sabit's user avatar
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2 votes
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Quantum simulation of molecular spectroscopy: why?

Molecular spectroscopy, e.g. through light-matter interaction, is a powerful tool to measure molecular properties such as bond lengths, energy levels, vibration frequencies, ... which give insights ...
m137's user avatar
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Energy of polyatomic molecular vibrations

I understand that the energies of a simple diatomic molecular vibration are equal to $E_n=(n+\frac12)\hbar\omega$, and I also know the accompanying eigenfunctions for these energies. I have also heard ...
slithy_tove's user avatar
7 votes
2 answers
837 views

Energy of molecular vibrations

I have just read that the energy of a molecular vibration with frequency $\omega$ has eigenvalues of $(n+\frac12)\hbar\omega$, where $n$ is the quantum number. However, this equation really surprises ...
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