Questions tagged [molecular-dynamics]
Molecular dynamics (MD) is an approach used for simulating dynamic processes through successive integration of Newton's equations of motion.
356
questions
1
vote
1
answer
58
views
Why doesn't Car-Parrinello molecular dynamics require an SCF calculation?
Reading the various terms of the Lagrangian in Car–Parrinello molecular dynamics, I'm trying to understand why there is not an SCF procedure hidden there.
In fact, it seems to me like the second term ...
- 21
0
votes
2
answers
47
views
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 ...
0
votes
0
answers
30
views
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 ...
- 1
0
votes
0
answers
10
views
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 ...
- 1
0
votes
0
answers
22
views
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 ...
0
votes
3
answers
57
views
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 ...
- 275
0
votes
0
answers
24
views
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, ...
- 132
21
votes
9
answers
5k
views
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 ...
- 442
0
votes
1
answer
64
views
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 ...
- 275
0
votes
0
answers
57
views
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} \...
- 23
0
votes
0
answers
27
views
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 ...
0
votes
0
answers
15
views
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 ...
2
votes
2
answers
74
views
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 (...
1
vote
0
answers
46
views
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 ...
- 895
6
votes
1
answer
496
views
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 ...
