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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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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56 views

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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Adding hydrogen from command line or through a python script to carbons only?

I am trying to find an easy to use tool to add hydrogen atoms to molecules in pdbqt format to carbon atoms only as I do not want to change the tautomeric state of the molecules, I tried rdkit, babel, ...
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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 ...
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244 views

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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178 views

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 ...
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90 views

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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75 views

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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38 views

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, ...
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141 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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73 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 ...
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53 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) ...
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188 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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896 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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503 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 ...
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169 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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185 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 ...
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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?
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117 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 ...
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239 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? ...
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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 ...
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88 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 ...
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147 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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1k 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 ...
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989 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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39 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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633 views

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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201 views

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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102 views

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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175 views

temperature set point maintenance with Langevin thermostat + shake algorithm

During the past ~4.5 years of my PhD, I have written an MD code, based largely on LAMMPS and NAMD, however reparallelized to suit my computational scenario better. One important thing to mention ...
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282 views

Error in MD simulation with Lennard-Jones potential in C, resulting in a lack of conservation of energy

I'm working on a MD simulation using the Lennard-Jones potential and the Velocity Verlet algorithm. The code compiles and runs, but the energy for each time step is not conserved; it decreases ...
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Beowulf Cluster For MD simulations

What would you recommend as an all-in-one cluster management software for a Beowulf cluster? We have about 7(most of them are 8 core machines and 1 is a 48 core machine) very good compute nodes in our ...
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Is resampling more accurate than block average for statistical analysis of data?

I'm working in laboratories where molecular dynamics data are almost always analysed usign block average as stated in the famous Allen and Tildesley book. We divide the datas in blocks of size $M$ on ...
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35 views

Modeling Coupling: vibrational,rotational, etc

I am trying to figure out how to deal coupling. I am trying to model a polymer chain. I have to deal with the angle between adjacent angles, dihedral angles, and vibration. I am able to compute all ...
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643 views

Choosing the correct Ewald sum parameters

I'm currently working with a system where the long range Coulomb interactions are described with the Ewald summation method. I am using DL_POLY Classic. The Ewald summation method used is described ...
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572 views

Ways to start ab initio MD from classical MD

I am running molecular dynamics simulations of water for testing purposes. The box is quite small, if you ask a guy running classical MD, and relatively large, if you ask a DFT guy: I have 58 water ...
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Why not solve molecular dynamics trajectories exactly?

The basis of Molecular Dynamics simulation is the integration of newton's equations of motion: $$\frac{F}{m} = \frac{d^2r}{dt^2}$$ I understand that there are various methods based on Taylor's ...
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84 views

Creating dense random configuration in for molecular dynamics

I am creating a random configuration of particles for a molecular dynamics simulation, where I would like to guarantee a certain density. The strategy is as follows: choose randomly the positions of ...
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181 views

Maxwellian distribution of velocities with Shake algorithm present

I am writing a code to perform hybrid monte carlo molecular dynamics. To do this, I need to have a code to initialize the velocities of all particles according to a maxwell distribution. The code is ...
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190 views

Effect of Periodic Boundary condition in Pair Distribution function

When we simulate a bulk molecular system using molecular dynamics in (say) NVE ensemble (microcanonical), we apply some periodic boundary conditions (PBC) to avoid surface effects. What effect does ...
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Fortran code for Ewald summation

I am trying to write a code to calculate the potential and forces, for the same using ewald summation.For this purpose, the formula for potential and force I have used is : $$ U = U^{(r)} + U^{(k)} +...
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305 views

Unfolding folded trajectories for Diffusivity calculation - MD

I have just started using dl_poly classic to work in Molecular Dynamics simulations. It produces a HISTORY file which records the trajectory after applying boundary conditions. Now, here I don't ...
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535 views

Molecular dynamics: Lennard-Jones forces in 2D system

As I am new to all these stuff I would like to verify whether my procedure is correct. I need to calculate the Lennard-Jones potential, potential energy of the system and the forces. The procedure ...
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2answers
528 views

Estimation of time taken to reach steady state in an MD simulation of Poiseuille flow

I am trying to do a Molecular Dynamics Simulation of a complex fluid, confined between solid surfaces. I would like to find the flow rate as a function of fluid film thickness, $h$, for a plane ...
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383 views

Generating random numbers for long molecular dynamics simulations

I've written a basic 2D Langevin dynamics simulator in C++, for a particle in a potential, solving the equation: $$M\ddot{X} = - \nabla U(X) - \gamma M \dot{X} + \sqrt{2 \gamma k_B T M} R(t)$$ This ...
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831 views

energy drift in molecular dynamics

I hope the following question will not be perceived as to vague. I am trying to ask the question directly, without going into too much information regarding my code. I am currently developing a ...
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periodic boundary conditions for triclinic box

I am trying to do analysis on a data set of atomic coordinates generated form lammps. I simulated an alpha glycine crystal in a triclinic box. The box vectors look like the following, where xy,xz,and ...
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71 views

Proper handling of 1-2 1-3 1-4 bonded neighbors in long range electrostatic solver

I have been wrestling with how to properly deal with bonded (1-2 1-3 and 1-4) particle neighbor interactions, or whether they have to be dealt with, in the long range electrostatic solver codes (PME, ...