All Questions
Tagged with computational-physics molecular-dynamics
18
questions
2
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2
answers
1k
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Understanding leapfrog integration algorithm
The leapfrog.cpp is an implementation of leapfrog integration algorithm where f() function is being integrated:
leapfrog.cpp
<...
- 75
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0
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50
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I encountered some issues simulating the shape transition of silicon clusters using LAMMPS
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I have been trying to write an input file for lammps to simulate the shape transition of a nanoparticle of silicon using multiple potentials to obtain the best structure, which I will compare with ...
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1
answer
1k
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Who can explain the minimum image convention in molecular dynamic simulations?
How to choose the cutoff radius so that the atoms do not interact with its periodic image? Especially when simulating macromolecules (proteins).
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Comparison of computational complexities of MD versus MC simulations
In my humble understanding MD simulations of systems with short-range(like LJ interactions) and long-range(electrostatic) has a computational complexity $O(N . log(N))$. What will be the computational ...
- 81
4
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2
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Time Reversibility of Velocity Verlet Algorithm
I'm very new to computational Physics and am finding conflicting statements on whether the velocity Verlet algorithm, defined as:
$\begin{align}
x_{n+1} &= x_n + v_n \Delta t + \frac{1}{2} a_n \...
- 141
1
vote
1
answer
72
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Which are the right configurations in the Markov chain of a Hamiltonian Monte Carlo algorithm?
I have a question about the Markov Chain Hamiltonian Monte Carlo (MCHMC).
Hamiltonian Monte Carlo is known as Hybrid Monte Carlo too. I'll describe the steps of the algorithm.
We have at the ...
- 113
1
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41
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Tackling multiscale problem in numerical simulation
In a dusty plasma system there are more than one component with different masses, i.e, electrons, ions,neutrals and dust grains. Accordingly, there are more than one temporal and spatial scales ...
- 19
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83
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Why this LJ molecular dynamics result doesn't converge?
I am doing a molecular dynamics simulation of Leonard Jones 6-12 potential. But instead of converging to a particular value. It always stays between -5.58 to -5.62. The standard value is -5.517. The ...
- 27
3
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1
answer
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Calculation of Mean Square Displacement for Brownian dynamics system with Lennard Jones interactions in python3
I have a problem getting a sensible result for the Mean Square Displacement (MSD) for a simulation of $N$ particles under Brownian dynamics with Lennard-Jones interaction between them with or without ...
0
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2
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110
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How to calculate $g_r$ when using the cell method algorithm
I have a self-written MD code in C++. I am simulating atoms using the Langevin dynamics model. I use the linked-cell method to speed up the simulation; as a result, atomic interactions are only ...
- 197
1
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2
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238
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Discussing the energy spectrum of Langevin Dynamics simulation of many atoms
UPDATED
I've coded a multiparticle MD simulation in 3D. It is based on Langevin Dynamics, with random impulse and dissipation. I think the program works correctly now? I have attached the plots of ...
- 197
2
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2
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908
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How to compute forces in multi-particle MD
Suppose we have a system of $N$ particles that interact via the Lennard-Jones potential $$V(r)=V_0\left[\left(\frac{r_0}{r}\right)^{12}-2\ \left(\frac{r_0}{r}\right)^{6}\right].$$ No other forces ...
- 197
1
vote
1
answer
280
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Oil/Water interface simulation using GROMACS
I would like to perform a decane/water(tip4p) interface simulation using GROMACS to analyse the fluctuation of the interface over a long period of time (50ps - 1ns).
Though I have a rough idea on ...
16
votes
1
answer
3k
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Why is leapfrog integration symplectic and RK4 not, if the latter is more accurate?
In a system where energy theoretically should be conserved, the most accurate simulation would conserve energy (as well as giving accurate positions, velocities and etc). RK4 is more accurate than ...
- 275
7
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1
answer
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How do I generate Maxwell-Boltzmann variates using a uniform distribution random number generator?
I am doing a molecular dynamics simulation. I need to assign initial velocities to the atoms. I want to assign the initial velocities which follow the Maxwell-Boltzmann distribution. How do I ...
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