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Questions tagged [molecular-dynamics]

Molecular dynamics simulations aim at solving the equations of motion of the atoms belonging to a molecular system using explicit time propagation and taking into account the effect of temperature on the atomic velocities (as opposite to geometry optimization). The interatomic forces can be described in classical (MM), quantum (QM) or mixed (QM/MM) frameworks.

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How conservation of momentum is ensured in (Projected) Gauss-Seidel constrain solver

I'm developing molecular dynamics where my time-step is limited by stiffness of the bonds. I trying to get inspiration from game-engines, where they solve similar problem (hard bond constrains). These ...
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How to embed linear elasticity/constrain solver in non-linear soft-body dynamics

I often do simulation of dynamics of mass points connected by strings (e.g. molecular dynamics, soft body dynamics etc.). Typically I do it simply by integration of equations of motion by e.g. verlet ...
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How do we calculate solvent accessible surface area (SASA) for a system simulated with annealing protocols in Gromacs?

I calculated SASA for 4 systems using the following command. The trajectory file (run.xtc) is not treated with gmx trjconv option. In my MD simulation, I followed two annealing cycles in each 50 ns ...
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Compute either only the attractive term or the repulsive term in Lennard-Jones

The Lennard-Jones potential is typically expressed mathematically as: $$ V(r) = 4 \varepsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^{6} \right] $$ where: $V(r)$ ...
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Where should we compute `Energy` and `Trajectory` in this listing?

Suppose, I have the following listing for a barebone MD simulation: ...
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Starting configuration for Molecular Dynamics

I have to build a bilayer using a structure obtained in a previous MD simulation. In the structure, some chains of the molecules cross the simulation box as shown below. I added water layers to the ...
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Computing LJ force from LJ potential, or not?

Lennard-Jones force can be computed in two different ways: Version #1: Here, the force computation is a self-contained routine. ...
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Am I doing leapfrog integration correctly?

I wrote this minimal example to examine the Leapfrog integration algorithm. However, I am not sure it is the correct algorithm, and the listing is giving the correct output. Is this the Leapfrog ...
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How can I write a unit test for this routine?

The first routine instantiates numAtoms number of atoms and distributes them in a 6*6*6 grid. The second routine populates the ...
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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 <...
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Example: Velocity Verlet reduced accuracy

Velocity Verlet is often held to far more accurate than forward Euler while being no more expensive. Technically, this requires some degree of regularity on the potential. But, is there a convincing ...
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I encountered some issues simulating the shape transition of silicon clusters using LAMMPS

== 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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why does the average temperature vary a lot from my setting temperature in nve?

I set my t_start and t_stop as 0.52 (lj unit), and I ran the nvt first. after it reached equilibration I ran the nve but found the temperature of the last 1000steps went up to 0.56 while my coworker ...
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Symplectic (or alike) integrator for system with Coulomb singularity and time-dependent potentials

I am trying to calculate classical trajectories for a single positive ion and a single electron inside an RF trap. Therefore, I am dealing with a two-body system that possesses: Coulomb potential ...
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Unit comparison between two molecular dynamics simulations with different time step

I need some clarification regarding the time step used in the molecular dynamics simulations. In the first simulation the time step was 1 nanosecond and in the second simulation the time step in 10 ns....
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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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How error scales with numerical precision in molecular dynamics?

In terms of time-step, numerical error in molecular dynamics scales with square, i.e. $error \approx dt^2$. But how it look for numerical precision ? E.g. how much bigger will be numerical error when ...
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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 ...
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Neighbor lists in overdamped Langevin MD simulations

The following question is about the implementation of molecular dynamics simulations with neighbor lists. In cases where the paths of individual particles are (i) stochastic and (ii) somewhat rough, ...
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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 \...
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Reference request: Textbook similar in structure to "Computational Materials Science: An Introduction" by June Lee for Computational Biology

In the Computational Materials Science: An Introduction by June Lee, he discusses molecular dynamics and density functional theory with examples from LAMMPS and QuantumEspresso, and explains LAMMPS ...
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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 ...
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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 ...
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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 ...
Endeavour 's user avatar
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The velocity Verlet method and variable time steps

Does the velocity Verlet handle variable time steps? I found controversial statements about it. In the paper Skeel, R. D., "Variable Step Size Destabilizes the Stömer/Leapfrog/Verlet Method", BIT ...
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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 ...
Constantine Black's user avatar
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Super Computer cluster service for students [duplicate]

I would like to ask whether there is a free of charge supercomputer for students, in my current institution they don't have a supercomputer, I am running MD simulations, I would be grateful for ...
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Langevin Thermostat and overdamped Langevin Equations

I'm having some difficulties understanding the Langevin thermostat (MD). In my notes, there is written that the Langevin equation is $$ m\dot{v} = F - m\gamma v + f_R, \tag{1} \label{1}$$ where $...
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Can LINCS algorithm be used for colliding molecules?

Supposing that one molecule is static and one is dynamic, can the dynamic one be solved with LINCS for its shape (angle, bond length) constraints and also keep collisions with static molecule off, ...
huseyin tugrul buyukisik's user avatar
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257 views

Custom exponents for Lennard Jones in LAMMPS

I am trying to run an MD simulation using this generalized version of Lennard Jones. $$ U(r) = \left(\frac{r_0}{r}\right)^A -\frac{A}{B}\left( \frac{r_0}{r} \right)^B $$ However, I do not know how ...
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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 ...
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Calculate forces on atoms from potential energy of system and position of atoms

Background I am using a neural network to calculate the potential energy of atoms in a configuration and then adding energy of all atoms to compare it with the true energy of the configuration(label) ...
fireball.1's user avatar
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2 answers
686 views

Effective way to build the neighbor's list in MD

I'm trying to implement the following form of the cell/neighbor list method in my MD code. I have divided my simulation box into a fixed number of cells, and according to its positions, I have ...
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Interatomic distance-periodic boundary conditions-non cubic unit cell

I am trying to find interatomic distance considering periodic boundary conditions for hexagon cubic cells (graphite). I tried to follow the answers to these two questions here but am unable to get the ...
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What good are hard-sphere event-driven molecular dynamics simulations in the face of chaos?

Simple hard-sphere dynamical systems can exhibit chaotic dynamics. Due to finite-precision arithmetic when implemented on a computer, the presence of chaos implies that for a given set of initial data,...
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1 answer
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MD Simulation: Reference for the Neighbor's List Method

With a rather basic knowledge in C++, I have written my own MD simulation code. Currently, I calculate forces in the most naive way: I go through all the atoms and account for their interactions. This ...
Ptheguy's user avatar
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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 ...
Ptheguy's user avatar
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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 ...
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Rigid and flexible ZIF-8 framework [closed]

What are the differences in parameters in the force field for MD simulation study of RIGID and FLEXIBLE ZIF-8 framework?Is the electrostatic interaction term present in the rigid one?
Piyali Mukherjee's user avatar
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1 answer
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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 ...
Ramanathan Varadharajan's user avatar
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Is there any scalable machine learning tool like molecular dynamics software NAMD?

I work in Molecular dynamics of biomolecules. I am familiar with the software NAMD. We use NAMD in our CPU cluster with the aid of mpirun. Without GPUs can I implement large scale deep learning? ...
dexterdev's user avatar
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How to implement boundary conditions in arbitrary geometries, in MD\Lagrangian FD simulations

Let's say I have a random arbitrary geometry, like this one https://ibb.co/dG8fUa (something I just made up). I make one of these in 3D in SolidWorks. I have molecules/particles coming in through the ...
Ayush Agrawal's user avatar
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Generate a set of random x,y,z numbers, with a minimum difference between them, between defined limits

So I am trying a molecular dynamics simulation, and trying to populate a 3D rectangular volume with random particles which are uniformly distributed throughout the volume. Each molecule has a fixed ...
Ayush Agrawal's user avatar
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1 answer
166 views

Why are Hamiltonian dynamics used in MCMC?

In Hamiltonian Monte Carlo, Hamiltonian dynamics are used to generate new proposals from the current state. I understand why these dynamics are used as opposed to random walk behavior to generate ...
ugabooga's user avatar
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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 ...
userManyNumbers's user avatar
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3 answers
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How to integrate numerically Nosé Hoover equation?

In NVT molecular dynamics, Nosé Hoover thermostat is a method defining an extended system. I can understand perfectly how the Nosé Hoover differential equations are derived (Frenkel&Smit's book). ...
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Forcefield for studying a two phase system, consisting of noble gases and gaseous organic components

I am preparing to do a MD-simulation of a system which consists of two phases. The gaseous phase consists of $H_{2}$, $Ar$, $He$, $N_{2}$, $CH_{4}$ and $CO_{2}$. In this system, $p=0.355 ~bar$ and $T\...
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How to control temperature in NVE molecular dynamics

I want to simulate a molecular system at a certain temperature. It would be best if it could be implemented by NVT molecular dynamics. However, if one were to use a NVE simulation (like velocity ...
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Fast Python implementation of short-range interacting particles under Metroplis algorithm

Can anyone write a Python implementation of a set of particles interacting in 2D according to a short-range particle-particle force and evolving in time under a Metropolis algorithm, which randomly ...
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List of Tersoff potentials?

I would like to know some GNU libraries or lists of downloadable Tersoff potentials. I couldn't find that many of them, and I also would like to know if there is a reason as to why this is the case.
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