Questions tagged [molecular-dynamics]

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

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35
votes
3answers
460 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)?
35
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2answers
388 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, ...
31
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2answers
340 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? ...
24
votes
2answers
2k 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 ...
23
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1answer
137 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 ...
21
votes
2answers
812 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 (...
21
votes
3answers
265 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 $U_{ij} = \frac{1}{2}k(r_i - r_j)^2$ ...
20
votes
2answers
130 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 ...
20
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1answer
127 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. ...
19
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5answers
2k 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?
19
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2answers
728 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 ...
19
votes
1answer
147 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 ...
18
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4answers
649 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 ...
18
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3answers
559 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 ...
18
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1answer
253 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 ...
18
votes
1answer
359 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 ...
15
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6answers
2k 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 ...
15
votes
3answers
172 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?
15
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1answer
323 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 ...
15
votes
1answer
119 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 ...
15
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1answer
169 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 ...
15
votes
1answer
158 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 ...
14
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2answers
243 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(...
14
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1answer
974 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 ...
14
votes
1answer
79 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 ...
14
votes
1answer
57 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 ...
14
votes
1answer
90 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 ...
14
votes
1answer
194 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 ...
14
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0answers
84 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 ...
13
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2answers
510 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 ...
13
votes
2answers
218 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 ...
13
votes
1answer
161 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 ...
13
votes
1answer
147 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 ...
13
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0answers
124 views

Empirically determining thermostat damping factor

Is there a way to determine an appropriate thermostat damping factor given a timestep size and a numerical integration method? I am computing a set of simulations in LAMMPS, using ReaxFF, tracking ...
12
votes
1answer
88 views

Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance

I am using an open source python package openmmtools to run a simple molecular simulation problem using the metropolis algorithm. I first load a default system of particles (alanine-dipeptide in ...
12
votes
1answer
266 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.
12
votes
1answer
74 views

Is it possible to parametize a nucleation model from molecular dynamics simulation?

I would like to build a nucleation model for Ti-6Al-4V by finding coefficients for the Avrami equation. Is it possible to estimate these coefficients (or find approximate error bounds for them) using ...
12
votes
1answer
52 views

What does this temperature & total free energy profile mean (obtained from VASP NVT molecular dynamics simulations)?

In order to obtain molecular dynamics (MD) simulations trajectory for computing phonon dispersion relation at finite temperature, I performed NVT MD simulation using VASP for my target system. Here is ...
12
votes
1answer
160 views

Analyzing MD trajectory: molecule orientation

I'm running a MD simulation (in Gromacs) of dye molecules incorporated into polymer to determine how that system responds to external electric field. There are two order parameters that are used to ...
12
votes
1answer
80 views

Rule-of-thumb for Morse potential cutoff in molecular dynamics?

Is there a rule-of-thumb for selecting a cutoff for the Morse potential in molecular dynamics simulation? For instance, is it typically some multiple of the equilibrium distance?
12
votes
1answer
101 views

Creating Interatomic Potential for Lammps using DFT

What are the basic steps and methodologies used in creating inter-atomic potential (specially EAM, MEAM potentials) for metals ...
12
votes
1answer
116 views

How much of a difference in a protein's radius of gyration can be considered significant?

In molecular dynamics simulations of proteins, the radius of gyration is often used to assess the compactness of a protein. When comparing two protein radius of gyration, what difference can be ...
12
votes
1answer
320 views

Compute RDF between COMs of two selections (or groups) using GROMACS

I have been using gromacs since years but I am always confused when I want to perform the following task: compute the RDF (radial distribution function) between the ...
12
votes
1answer
92 views

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 ...
12
votes
0answers
123 views

Sample LAMMPS file for graphene growth on a metal surface [closed]

I am working with graphene growth on metal substrates. But I need some sample files to know if I am doing it in the right way because running multiple simulations in LAMMPS takes a lot of time. Can ...
12
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0answers
113 views

Poiseuille flow by LAMMPS [closed]

I am trying to model 3D Poiseuille flow of an argon gas confined between two parallel platinum plates by using LAMMPS. I have one reference paper, as given in [1] below. I built my platinum structure ...
11
votes
3answers
401 views

Which ensemble to use for a molecular dynamics simulation?

Does it matter which ensemble you use for a molecular dynamics simulation? Shouldn't they in principle give the same results? Why, historically, was it hard (and desirable) to develop simulations in ...
11
votes
1answer
210 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
11
votes
1answer
134 views

How does one compute the boiling point of a liquid made of a particular molecule?

This question is in relation to Anomalous boiling point of "iso-" alkanes on Chemistry SE. I want to compute the boiling point of the different isomers of an n-carbon alkane to check what ...
11
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2answers
61 views

What is the most appropriate (and easy-to-use) all-atoms force field for liquid electrolytes?

I need to simulate a salt diluted in a liquid electrolyte. My experience is with LAMMPS, but so far I only had coarse grained toy models, and setting up the force field was straightforward. Now I have ...