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Questions tagged [molecular-dynamics]

For questions related to the use of or theory behind classical or ab initio molecular dynamics.

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43 votes
4 answers
8k views

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, ...
BernhardWebstudio's user avatar
37 votes
2 answers
991 views

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? ...
exsonic01's user avatar
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36 votes
3 answers
1k views

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)?
TheSimpliFire's user avatar
31 votes
2 answers
4k views

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 ...
Barbaud Julien's user avatar
26 votes
2 answers
3k views

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 ...
Paulie Bao's user avatar
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26 votes
1 answer
358 views

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 ...
jheindel's user avatar
  • 3,584
25 votes
2 answers
1k views

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 (...
jheindel's user avatar
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24 votes
5 answers
4k views

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 ...
epalos's user avatar
  • 4,879
24 votes
1 answer
3k views

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 ...
jheindel's user avatar
  • 3,584
23 votes
3 answers
1k views

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 $U_{ij} = \frac{1}{2}k(r_i - r_j)^2$ ...
James Flash's user avatar
22 votes
6 answers
4k views

What software is available to do molecular dynamics on Windows?

Is there a Windows-based molecular dynamics simulation software which is easy to use?
Papia Chowdhury's user avatar
22 votes
3 answers
2k views

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 ...
epalos's user avatar
  • 4,879
21 votes
1 answer
187 views

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. ...
Gabriel Olguín's user avatar
20 votes
2 answers
1k views

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 ...
mykd's user avatar
  • 2,352
20 votes
2 answers
227 views

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 ...
n7ype's user avatar
  • 303
19 votes
1 answer
668 views

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 ...
NTS's user avatar
  • 759
19 votes
1 answer
326 views

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 ...
Emil Zak's user avatar
  • 896
18 votes
2 answers
1k views

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-...
megamence's user avatar
  • 4,171
18 votes
3 answers
781 views

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?
Meilani Wibowo's user avatar
18 votes
2 answers
2k views

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.
Rashid Rafeek's user avatar
18 votes
1 answer
1k views

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 ...
Achintha Ihalage's user avatar
18 votes
1 answer
374 views

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 ...
lcdumort's user avatar
  • 283
18 votes
1 answer
1k views

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 ...
Achintha Ihalage's user avatar
18 votes
1 answer
391 views

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 ...
geo's user avatar
  • 455
18 votes
1 answer
940 views

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 ...
DGKang's user avatar
  • 920
17 votes
4 answers
4k views

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 ...
NickZ's user avatar
  • 1,509
17 votes
3 answers
3k views

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 ...
littleworth's user avatar
  • 1,674
17 votes
1 answer
198 views

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 ...
nathanielng's user avatar
16 votes
2 answers
7k views

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 ...
2ndQuantized's user avatar
  • 1,021
16 votes
2 answers
1k views

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 ...
Pranav kumar's user avatar
  • 4,306
16 votes
1 answer
6k views

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 ...
SaiSmaran S B PES1201701189PES's user avatar
16 votes
1 answer
188 views

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 ...
Magic_Number's user avatar
15 votes
6 answers
4k views

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 ...
John T's user avatar
  • 666
15 votes
3 answers
3k views

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?
Carlos Andrés del Valle's user avatar
15 votes
2 answers
905 views

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(...
Kavya Mrudula's user avatar
15 votes
1 answer
196 views

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 ...
BernhardWebstudio's user avatar
15 votes
1 answer
189 views

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 ...
SalvaCardona's user avatar
  • 1,590
15 votes
1 answer
750 views

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 ...
user avatar
14 votes
3 answers
617 views

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 ...
Barbaud Julien's user avatar
14 votes
2 answers
830 views

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 ...
user avatar
14 votes
2 answers
644 views

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
2ndQuantized's user avatar
  • 1,021
14 votes
1 answer
540 views

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 ...
mykd's user avatar
  • 2,352
14 votes
1 answer
121 views

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 ...
Kavya Mrudula's user avatar
14 votes
0 answers
108 views

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 ...
anneb101's user avatar
  • 995
13 votes
3 answers
5k views

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.
littleworth's user avatar
  • 1,674
13 votes
2 answers
572 views

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 ...
Kavya Mrudula's user avatar
13 votes
2 answers
2k views

Using the VACF command in LAMMPS to get the velocity autocorrelation function

I am writing a simple Lennard-Jones fluid simulation in LAMMPS. So far, I have outputted the temperature, volume, density, total energy, enthalpy, pressure, and all of it seems to be believable every ...
megamence's user avatar
  • 4,171
13 votes
1 answer
432 views

Are there any MD packages that do proper free energy sampling in the NPT ensemble?

Statistical Mechanics is the basis of molecular level calculations of properties and averages. Nowadays free energy calculations are fairly "turn-the-crank", which is not necessarily a good ...
B. Kelly's user avatar
  • 4,386
13 votes
2 answers
913 views

Phase transition in Molecular Dynamics simulations

I am reading the book Computer Simulation of Liquids[1] where on multiple occasions it says MD is valid as long as the conditions simulated are away from phase transition. For example, at the ...
Gotaquestion's user avatar
13 votes
1 answer
2k views

What does the Neighbor command do in LAMMPS?

I frequently see LAMMPS codes, and almost all of them have the neighbor 0.5 bin command. I completely studied the LAMMPS manual for the neighbour command and did ...
SaiSmaran S B PES1201701189PES's user avatar

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