Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
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Modelling Diffusion of Molecules Through a Physical Barrier
I would like to model the diffusion of various small molecules (e.g. $\ce{O2}$, $\ce{H2O}$, $\ce{MeOH}$, etc.) through polymeric barrier material (e.g. polyethylene, ethylene vinyl alcohol, ...
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Does the Hamiltonian of an unbiased simulation change when the simulation moves from a stable basin to another?
I wanted to understand the change in the Hamiltonian function as an unbiased simulation goes from one stable basin to the other.
Does the Hamiltonian stay constant or does it change as the unbiased ...
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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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What is the "overcoherence problem" in Ehrenfest dynamics?
I am a novice in Ehrenfest dynamics and would like to know why Ehrenfest dynamics suffers from the "overcoherence problem"?
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What is the difference between Ehrenfest dynamics and Born-Oppenheimer Molecular Dynamics? [duplicate]
What is the fundamental difference(s) between Ehrenfest dynamics and Born-Oppenheimer MD? Also, in what situation(s) or case(s) one is preferred than the other one?
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Calculate free energy for a canonical (NVT) ensemble [closed]
Note: Users wishing to answer this question may write a comment or a message in the chat indicating their desire for the question to be re-opened.
I have an NVT ensemble of water molecules (liquid) ...
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What are the factors to consider before docking 2 proteins?
With no background in biological science, I need help with docking 2 proteins together. This issue is with regards to SARS-CoV-2. The 2 proteins are Spike glycoprotein and membrane protein. What are ...
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Setting multiple new atype/dtype/itype with LAMMPS fix bond/create [closed]
When creating a new bond in a LAMMPS simulation with the command fix/bond create it is likely new angles/dihedrals/impropers be need to be set. This can be done with the atype/dtype/itype arguments ...
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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 ...
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Why am I losing bonds when I use PACKMOL on two proteins?
I recently started using PACKMOL to pack a few proteins together. I wrote this PACKMOL code:
...
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LAMMPS code that I wrote not behaving as expected. Some issue with the group & region commands
I am actually working on SARS-CoV-2 proteins. Specifically I am trying to tribologically disengage the Spike Glycoprotein from the Membrane protein using LAMMPS. The method is to use amorphous carbon ...
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What are the types of Quantum Molecular Dynamics (QMD)?
In similar spirit to recent questions on Quantum Monte Carlo, ab-initio Molecular Dynamics, types of SCF, and others, I would like to ask:
What are the types of Quantum Molecular Dynamics (QMD)?
As I ...
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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 ...
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How can I calculate the Poisson ratio of an amorphous material with LAMMPS?
I noticed that we can calculate the Poisson ratio of a crystalline metals with LAMMPS. I wonder if we can use that example for a metallic glass! If no, is there any other way, with another software?
user1099
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Dealing with symmetry of ordered primitive cell during DFT structure relaxation
I have a large disordered cubic structure that I would like to do AIMD on to look at cation diffusion. I found the primitive cell and then ordered it to create several configurations. I will then ...
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I wrote a Python code to do MD for a Lennard-Jones fluid but the VACF is wrong: What might be the problem? [closed]
I am trying to write a molecular dynamics simulation for a Lennard-Jones fluid in a box with periodic boundary conditions. The box has no net momentum. I am writing this in python.
I have written a ...
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Calculating diffusion coefficient from Mean Squared Displacement
I am performing a molecular dynamics simulation and I have calculated the velocity autocorrelation function (VACF), $\psi (t)$ and mean square displacement, $\langle (\Delta r)^2 \rangle$. In my ...
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What are some methods for modeling bulk phase infrared spectra?
I am interested in predicting the infrared spectra of bulk phase molecules, it seems that AIMD (ab initio molecular dynamics) is the current best approach. I have found a tutorial on using CP2K to do ...
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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 ...
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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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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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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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How do I generate an aluminum force-field for a LAMMPS input file? [closed]
I have been assigned a project on the generation of a force-field of Al (aluminum) for a LAMMPS potential.
I have no idea how to proceed and what to do next. Can anyone please let me know how should I ...
21
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1
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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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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 ...
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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 ...
12
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1
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3D Poisson equation solver for arbitrary charge distribution?
I am trying to compute the electrostatic potential profile from a distribution of point-charges that were output from an MD simulation. Does anyone know of ready-made Poisson solver packages that are ...
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1
answer
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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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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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Can you model Radiation Chemistry with existing MD software?
I'm wondering if it is possible to simulate the chemical changes materials undergo when exposed to ionizing radiation for a finite period of time with Molecular Dynamics (MD) software. In principal ...
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Is it possible to use the Parrinello-Rahman barostat for NPT simulations in CP2K?
It is possible to use different types of thermostats in CP2K by specifying them in the corresponding section of the input as mentioned here. But there is no mention of specifying the barostat type in ...
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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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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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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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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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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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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?
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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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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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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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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 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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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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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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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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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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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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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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answer
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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 ...
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