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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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41 views

### Green-Kubo Relation

I am calculating the viscosity of WCA fluid using the Green-Kubo relation. I am also following the paper of Zhang et al. for the Time decomposition method where they fit an analytic function to the ...
35 views

### 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 ...
35 views

### 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 ...
53 views

### 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 ...
• 21
1 vote
38 views

### 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: $V(r)$ ...
64 views

### Where should we compute Energy and Trajectory in this listing?

Suppose, I have the following listing for a barebone MD simulation: ...
170 views

### 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 ...
• 21
1 vote
79 views

### 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. ...
127 views

### 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 ...
1 vote
106 views

### 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 ...
1k views

### Understanding leapfrog integration algorithm

The leapfrog.cpp is an implementation of leapfrog integration algorithm where f() function is being integrated: leapfrog.cpp <...
70 views

### 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 ...
34 views

### 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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63 views

### 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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31 views

### 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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1k views

### 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).
155 views

### 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 ...
78 views

### 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 ...
33 views

### 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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### 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, ...
1 vote
263 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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112 views

### 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 ...
• 207
230 views

### 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) ...
• 131
740 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 ...
• 207
2k views

### 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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2k views

### 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 ...
• 207
1 vote
238 views

### 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 ...
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918 views

### 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 ...
• 207
1 vote
22 views

### 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?
1 vote
280 views

### 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 ...
281 views

### 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? ...
1 vote
45 views

### 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 ...
103 views

### 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 ...
167 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 ...
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3k views

### 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 ...
1 vote
2k views

### 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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61 views

### 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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1 vote