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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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 ...
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How does a knife cut things at the atomic level?
As the title says. It is common sense that sharp things cut, but how do they work at the atomical level?
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Deuterium density in seawater
I heard today that deuterium for nuclear fusion could be extracted from the Oceans, in which it is present in "heavy water." I heard this claim:
"Deuterium is distributed uniformly with Ocean depth....
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Temperature and kinetic energy of molecules
I was wondering if temperature is related to the average translational kinetic energy of the molecules then why does the average kinetic energy of say a moving object not affect the temperature? What ...
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Can we fully simulate molecular physics?
Is our knowledge of physics complete enough to achieve fully natural simulations of molecular interactions in a computer simulation? How far off are we?
Reason for question: I wonder how far we are ...
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Born-Oppenheimer separation in Dirac bra-ket notation
Most derivations I have seen of the Born-Oppenheimer approximation are made using wave-functions. To understand it better, I was trying to write a derivation using Dirac notation, but I am stuck. I am ...
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Why do atoms repel when closer but attract when farther apart?
I was wondering why atoms, when pulled apart and then released, attract together, but I notice that there is a special distance at which this attractive force doesn't seem to act but rather those ...
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What happens if a metal wire that was one-atom in thickness was pulled across a finger?
What would happen if a metal wire that was one-atom was pulled across your finger? Would it cut off your finger, or would it pass through your finger without harming you? What if the metal one atom ...
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Why are large speaker cones required to to produce loud low frequency sounds?
Is there any reason for why a small speaker cone cannot produce low end sound at a comparable volume to higher frequencies?
I can understand how a larger speaker would be in contact with more air and ...
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Hamiltonian Monte Carlo: Kinetic and Potential energies
In HMC (good intro here) the Hamiltonian is defined as
\begin{align}
H(p,\theta) &= -\log p(q,\theta)
\\
&= -\log p(q) - \log p(\theta).
\end{align}
Here $p$ is the momentum coordinate and $\...
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Why aren't Runge-Kutta methods used for molecular dynamics simulations?
One of the most used schemes for solving ordinary differential equations numerically
is the fourth-order Runge-Kutta method. Why isn't it used to integrate the equation of motion of particles in ...
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How can fast moving particles gain energy from slow moving ones?
Imagine a large diameter piston filled with water connected to a small funnel. When you press on the piston slowly but with considerable force the water will move very quickly from the funnel in form ...
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Why is the canonical ($NVT$) ensemble often used for (classical) molecular dynamics (MD) simulations?
Molecular dynamics (MD) simulation is a common approach to the (classical) many-body problem. It relies on integration of Newton's equations of motion to simulate the trajectories of many (e.g., ~1,...
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Molecular Dynamics Software for Coarse Grained Polymers
I am looking around for MD software that I can use to simulating polymers and I can't decide which software I should use.
I would like to simulate the swelling of crosslinked polymers, and I would ...
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How can I include variable particle number in a Brownian dynamics simulation?
I programmed a Brownian dynamics simulation in two dimensions.
(Coarse-grained proteins on surfaces with interaction potentials i.e. patchy particles.) Now I want to allow particles to leave or enter ...
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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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Pressure inside a box with only a single molecule
Suppose that we have a cube with dimensions $25 \times 25 \times 25$ centimeters containing a single hydrogen molecule. How can we calculate the pressure within the cube?
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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 ...
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What is water pressure, really? [duplicate]
It's easy for me to imagine gas pressure on a molecular level. More pressure means that more molecule bounce against the thing you are measuring, or the molecules hit it with more speed or the ...
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Why is detailed balance required for thermodynamic consistency?
why does the Wegscheider condition or detailed balance have to be true for chemical reactions and what does it mean to violate it in terms of thermodynamics?
here is an attempt to derive a simple ...
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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 $...
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Integrating Langevin Dynamics equations in computer simulation
In a Langevin Dynamics simulation the following equation is solved numerically :
$$
m_i\frac{d^2r_i}{dt^2}=F_{int}-\gamma\frac{dr_i}{dt}+R(t)$$
$$\langle R(t)\rangle=0 \quad \quad \langle R(t)R(t')\...
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What actually makes boiling happen?
Boiling can be breezed over easily with a few rudimentary diagrams and a couple equations, but I seek a deeper explanation.
The definition of boiling is that the vapor pressure in the liquid is ...
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Symmetry in program for ewald summation
The formula for Ewald summation as given in Allen and Tildesley -
$$
U = U^{(r)} + U^{(k)} + U^{(bc)} + U^{self}
$$
where the k-space contribution of potential is given by
$$
U^{(k)} = \frac{1}{\pi ...
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Franck Condon Principle and Born Oppenheimer approximation
My question here is purely fundamental. I am confused with the concept in Franck Condon (FC) principle and Born Oppenheimer (BO) approximation. The FC principle is in accordance with the BO ...
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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 ...
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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{...
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Will "water" glow at very high temperatures?
I was chatting with my kids about how incandescent lightbulbs work, clarifying that they don't so much "burn very slowly" (their original understanding) so much as they emit photons "...
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Why collisions with other molecules not taken in account here?
I have few doubts related to this derivation
why collisions with other molecules not taken into account since they could also influence the time it takes for one molecule to collide with the wall
how ...
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Generating X-ray diffraction patterns from atomic coordinates
I have a list of atomic coordinates for a periodic system as a result of a molecular dynamics simulation. I want to use those coordinates and predict what it's 1D diffraction pattern looks like.
The ...
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Structure factor calculation for non-cubic lattices
I have an equilibrated trajectory from a molecular dynamics simulation and I would like to calculate the structure factor using the atomic positions. I think I am able to do it right for cubic ...
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Particles in a box simulation of vacuum system; how to treat scattering from walls? [closed]
note: I expect that a microscopic treatment of the rate of heat transfer between gases and solid surfaces will likely need to address this as well and so I'm looking in to that today, but if someone ...
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LAMMPS: How to enter a simple potential for Dissipative Particle Dynamics (DPD)?
I apologize if this is off-topic and if so would be grateful for someone to point me to a relevant source of information.
Dissipative Particle Dynamics (DPD) is a quick simulation technique that ...
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When do gas molecules deviate from Maxwell Boltzmann distribution?
The velocity of the gas molecules at room temperature obey Maxwell Boltzmann distribution. When we say velocity, the distribution is true for each component right ? means vx, vy and vz are in MB ...
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Electric diagonal rail for rockets/space shuttle using a modified E-fan [closed]
Can a series of blimps be aligned to evenly distribute the weight of an electric track 95% not load bearing for a winged rocket like a cruise missile to to be carried by a guide and E-fan up to the ...
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Is there instantaneous communication inside a quantum entity?
This question also stems from Anna's answer here: https://physics.stackexchange.com/a/578929/230132
Quoting her, she says an electron bound to a nucleus is not a quantum entity, the entire atom is. ...