Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
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How should one choose the time step in a molecular dynamics integration?
Choosing too small of a timestep leads to an unrealistic simulation time, whereas too big of a timestep leads to the system not being represented correctly (or, in the case of an algorithm like SHAKE, ...
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In molecular mechanics, how are van der Waals forces modelled?
In terms of energy, how are van der Waals forces modelled (are there formulas/laws that govern these)?
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Machine learning interatomic potentials for molecular dynamic simulations: are they good?
I know the general question of machine learning in computational chemistry has been already raised here: What is the current status of machine learning applied to materials or molecular systems?
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Can a highly-cited published paper have this type of error?
Related cross-network post: Have there been instances in physics where different scientists have interpreted the same data differently?
Here is my problem: I have been testing a force field published ...
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What are the "smart algorithms" applied to solve the "curse of dimensionality"?
The "curse of dimensionality" is an ubiquitous issue arising in both electronic structure and quantum molecular dynamics, which refers to the exponential scaling of computational cost with ...
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Benchmark Timings of Machine Learning Potentials vs Molecular Mechanics Force Fields
Machine learning is an increasingly common tool for developing force fields for molecular dynamics simulations. It's not totally clear what should be considered a machine-learning potential, but let's ...
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Why do people care about reversibility in molecular dynamics simulations?
When carrying out a molecular dynamics simulation, one has to choose an ensemble. Depending on the problem, one usually works in the microcanonical (NVE), canonical (NVT), or grand canonical ensemble (...
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Simulating breaking bonds in molecular dynamics
How does one introduce the possibility of breaking a bond in a molecule during MD simulation?
I only found the cases when we just introduce the harmonic potential $U_{ij} = \frac{1}{2}k(r_i - r_j)^2$ ...
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How exactly does one compute the vibrational density of states from the output of a molecular dynamics simulation?
There are many things that can be done with the output of a molecular dynamics simulation, but one of the more powerful things is the ability to compute the vibrational density of states (or the ...
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What software is available to do molecular dynamics on Windows?
Is there a Windows-based molecular dynamics simulation software which is easy to use?
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References for Molecular Dynamics?
I am new to the world of Molecular Dynamics (zero practical experience), and I know that a starting point to really go into the back-bone of MD is Statistical Mechanics (took a semester course in ...
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Why can't I reproduce the behavior of an H-saturated graphene flake?
I'm trying to simulate a graphene flake with its edge C atoms saturated by H atoms, in a temperature ramp from 300 K to 1600 K, using LAMMPS and the AIREBO potential proposed by Stuart et al. in 2000.
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Does increasing Lennard-Jones cutoff means higher accuracy?
I am currently trying to simulate a large box of QM/MM water molecules with SPC/Fw model and GGA DFT functional (a cube of 40 angstrom sides). To validate the QM and MM simulations separately, I am ...
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What are the types of ab initio Molecular Dynamics?
I am new to the world of Molecular Dynamics, and am curious to know exactly what is considered to be an ab initio Molecular Dynamics (AIMD) method, and how do they work?
The seminal work by Roberto ...
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How to choose replica exchange interval?
I was wondering what goes into the consideration of choosing the frequency to attempt swaps for replica exchange? D. Sindhikara, 2008 proposes the faster the better, but this goes against the view ...
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Quadrature over three Euler Angles for orientation averaging
Does anybody know about an accurate quadrature rule over three Euler angles $\theta, \phi, \chi$?
I am trying to calculate the average value of an arbitrary function $f(\theta, \phi, \chi)$ for a ...
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Flying ice cube effect in molecular dynamics?
I am trying to understand what exactly the flying ice cube effect is, and how it manifests itself in MD simulation.
From what I have read about it, I see that as we run certain forms of velocity-...
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Does anyone know any software for MD simulation which include the effect of magnetic field?
I am interested to generate some configurations from MD simulations which include the presence of strong magnetic field. Does anyone know any software that has some functionality to do this?
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Computing phonon dispersion from molecular dynamics simulations?
How would one obtain the phonon dispersion curve from a molecular dynamics simulation trajectory? What are the steps involved? Are there any packages that does this? If so, please mention them.
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What are the ways to ensure thermodynamic stability of a DFT modelled new structure?
One way of predicting the thermodynamic stability of a DFT modelled structure is to calculate the energy above convex hull, which was used as the criterion in The Materials Project database. For ...
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How to optimize zinc oxide bulk structure at certain pressure with LAMMPS
I am trying to simulate the Zinc oxide bulk structure (periodic) at constant pressure(0.0 ~ 20.0 GPa) to observe phase transition with LAMMPS.
However, I approached a problem that the fluctuating ...
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I am considering to purchase a GPU. What calculations would need FP32, and what would need FP64?
I would like to know how to choose the best GPU on the basis of its FP32 or FP64 efficiency, depending on different types of simulations.
In brief I would like to know what types of simulations work ...
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What does ns/day mean in high-performance computing?
In MD simulation benchmarking, you often see performance expressed in terms of ns/day and hours/ns.
How do I translate these ...
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Is there a way to obtain solution-phase dielectric constants?
I wish to calculate solution-phase dielectric constants (required for a Monte-Carlo model) for CoCl$_2$ and TaS$_2$ dissolved in DMF.
Is it possible to estimate these constants from the solid-state ...
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Empirically determining thermostat damping factor
Is there a way to empirically determine an appropriate thermostat damping factor given a timestep size and a numerical integration method? For example, I would like one for the surface and the ...
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Classical Monte Carlo vs. Molecular Dynamics
Both Classical Monte Carlo (MC) and Classical Molecular Dynamics (MD) simulations are used to perform simulations of ensembles of molecules. These MC calculations are calculating thermodynamic ...
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How may I create an interatomic potential using DFT?
What are the basic steps and methodologies used in creating inter-atomic potential (specially EAM, MEAM potentials) for metals ...
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What are the advantages of (semi)-empirical force fields over Machine Learning Potentials?
I am currently working with ReaxFF, an empirical reactive force field that can describe chemical bond forming and breaking. The main advantage over ab initio methods are of course the greatly ...
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Is there any reason not to sum the kinetic and potential energy from an NPT simulation to get internal energy?
I would be very grateful for some newbie-level advice from a thermodynamics guru.
I ran NPT simulations on a particular system (in CP2K software) to get fluid densities for use in fluid dynamics ...
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Why do interaction potential parametrizations of bulk systems not work for corresponding nano-systems?
I am studying several thermodynamics properties of crystalline iron oxides ($\ce{Fe3O4}$, $\gamma-\ce{Fe2O3}$) in their solid phases by MD simulations. At the moment, I am facing many difficulties in ...
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How do I simulate the interaction between two atoms?
I want to build a rough atom interaction simulator, where pushes two (or more) atoms toward each other and they should behave physically correctly: attract, bond or repel with some force. So that is ...
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Can DFT simulate chemical reactions?
I was wondering, can you simulate the chemical reaction between two or more molecules using DFT? If not, what numerical method is usually used for this?
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What are the parameters that need to be calculated to design the structure of a molecule?
Before performing Molecular Dynamics on a co-polymer that doesn't have a ready-to-use structure anywhere, the monomer fragment was built in Avogadro software with 0 net charge, B3LYP theory and 6-31G(...
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How to rectify the error "Lost atoms: original 28437 current 3659" in LAMMPS?
I have modeled a complex structure of a protein and a Carbon nano-cone (used as an indenter to the protein) using PACKMOL. The LAMMPS data file of the complex structure consists of 4 atom types (C O N ...
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Ab initio molecular dynamics to check material stability at finite temperature
I completed an ab initio molecular dynamic (AIMD) simulation in VASP for a hypothetical material. The simulation was done for 5ps with 1fs steps and the temperature was set to 300K using Nosé–Hoover ...
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Can Newton's Equation of Motion be Integrated Analytically for Certain Chemical Systems?
In molecular dynamics, one typically integrates Newton's equation of motion, for example using a leap-frog algorithm. Are there chemical systems, for which an analytic integration is a viable ...
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Modeling vibronic interaction beyond Born-Oppenheimer
Within Born-Oppenheimer approximation, the motion of atomic nuclei are considered as being separated from the electrons movement. Although in general this approximation is valid for a high number of ...
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Minimum image convention for non-orthorhombic unit cells
I am trying to take into account periodic boundary conditions for non-orthorhombic unit cells.
I have the atomic coordinates for a monoclinic super cell with the following lattice vectors output by ...
user2026
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MD: How to estimate number of timesteps to converge a property
If I want to equilibrate a NPT system until a property reaches its equilibrium value (let’s say the volume V), what is the common practice to have a rough estimate of the total simulation time ...
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How do you incorporate hydrogen bonding into molecular simulations?
How do computer simulations of liquid hydrogen-bonding systems incorporate hydrogen bonding? Since I think hydrogen bonding has mixed covalent and electrostatic character, wouldn't you need something ...
user2026
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What are good resources to learn Materials Modeling?
I wonder if there are any books or resources to start learning Materials modelling using methods
density functional theory
quantum monte carlo
molecular dynamics
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Visualizing MD generated electron density cubes as trajectories
During an ab-inito MD simulation one can generate the electron density cube file which basically provides the electronic density data in a standard volumetric format as shown here. The file consists ...
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How can I decide on the order of different monomers in a co-polymer?
While performing molecular dynamics simulations on a co-polymer, how long should the minimum size of the polymer be, to replicate the experimental properties with a reasonable error?
Within this ...
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Generating interatomic potentials via force matching [closed]
I am trying to learn best practices for force matching ab initio molecular dynamics (AIMD) data with nonlinear least-squares minimization to generate interatomic potentials for use in classical MD.
I ...
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What does "force field" mean?
In MD simulations we often hear the term force field.
What is it?
We know, for example that, Gromacs provides various types of forcefields.
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Quantum chemistry in external electrostatic field?
Which quantum chemistry methods can be used in an external electrostatic field? Also which software supports that? I'm interested in anything from semiempirical (eg XTB) to DFT (eg ωB97, B3LYP-D3) ...
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How to find out the total functional form of the forcefield that is being used for a current simulation in GROMACS?
This is a doubt regarding the usage of various forcefields together in MD simulation of hydrates. For Eg., we use TIP4P/ice for water molecules, OPLS-UA for methane and EPM2 for carbon dioxide and so ...
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Recent developments in QM/MM for Molecular Dynamics
I am looking for new QM/MM methodologies which have recently developed and implemented into MD packages. Any applications or molecular systems studies with these methods can be used as an example as ...
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Applicability of GFN-FF force field and other xTB methods for dynamics of ions in water [closed]
I am working on a project involving water clusters with ions in them. One of the problems that I ran into quite early on was that good forcefield parameters are not available for highly charged ions ...
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How to calculate RDFs for MD trajectories without PBC, directly from coordinates? [closed]
I have been running MD simulations on water droplets with an ion in them. I am trying to implement a program that could calculate the radial distribution function from ion to oxygen (or ion to ...
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