Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
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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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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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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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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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Basics of numerical energy minimization techniques used in molecular dynamics?
The question below describes my plan to make a basic molecular dynamics calculation using a Python script rather than a canned, self-contained program.
There seems to be three parts:
a model of the ...
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DIY molecular dynamics for Xenes on crystal surfaces; where can I get applicable open-source force field parameters that I can use in my scripts?
The linked question(s) below describes a DIY project to simulate how Xenes (honeycomb nets of atoms like graphehe) behave on single crystal surfaces. Behaviors include rotation, strain, and heigh ...
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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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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 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 would one find a material's equilibrium structure at any specific temperature?
Let's take an example of a simple FCC material, a binary alloy. Above absolute zero K, the alloy will start to disorder and become an FCC solid solution. The alloy would develop defects as it ...
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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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Selection of appropriate Langevin damping parameter for MD of solid metal
I am performing an MD simulation involving solid metal. The system is in the NVT ensemble, and I am using the Langevin thermostat (fix Langevin in LAMMPS) to enforce this.
I have previously used the ...
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Starting configuration for a molecular simulation
When doing a computer simulation, what’s the best way to prepare a starting configuration to avoid biasing your results?
The book Computer Simulation of Liquids suggests putting the molecules on an ...
user2026
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How to choose between Molecular Dynamics and Monte Carlo when beginning to simulate either equilibrium or non-equilibrium systems?
Answers to Are MD and MC both able to study both equilibrium and non-equilibrium systems? include lots of examples pointing to "yes".
I'm currently faced with a task of modelings small ...
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Parameterize a complex that contains Transition metal (Build Force Field)?
It is a general question. I know, but I need some help.
I am interested to parametrize a complex that contains transition metal like Ru and Pt etc.
Furthermore, I will use this Force Field to do ...
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How to calculate the volumetric energy density of a molecule?
I am trying to store hydrogen in a hydrocarbon.
The example can be taken as cyclohexane ($\ce{C6H12}$) which is in a hydrogen-rich state. Its hydrogen-lean state is Benzene.
I want to calculate the ...
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How to make input script file for nanoparticle using LAMMPS?
Hope you're all doing well. I am a student of Doctorate in Beijing Institute of Technology. We are working on a project "DNA Regulated Nanozyme". and we intend to build an interaction ...
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Understanding derivation of discretized FIRE algorithm
Introduction/Preamble
@SusiLehtola's answer to Basics of numerical energy minimization techniques used in molecular dynamics? mentions conjugate gradients, BFGS for energy minimization, Metropolis ...
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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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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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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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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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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 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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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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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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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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How can one computationally determine the flammability of a molecular system?
I can imagine one aspect of flammability (the ability of a substance to ignite on fire) to include calculating the kinetics and thermodynamics of the reaction of the system with oxygen. This is not ...
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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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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 ...
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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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What kind of systems do we need to coarse-grain to observe interesting phenomena?
When I go to talks, I hear the statement "coarse-graining is required to access spatio-temporal scales to observe important dynamical behavior for stimuli-responsive systems" before they go ...
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Deviation caused by using DFT in Non-Adiabatic Molecular Dynamics
To calculate the excited state properties and processes of semiconductors (e.g. during the photocatalysis process), can be important. Non-Adiabatic Molecular Dynamics (NAMD) is one of the popular ...
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Unable to recreate data for benzene from paper in GROMACS 2020.5
I have been trying to simulate benzene in OPLSS-AA forcefield as per this paper: https://pubs.acs.org/doi/10.1021/ct2002122. I have been at a loss, since I believe I have everything running as per the ...
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How should I generate a radial distribution function (RDF) for an MD trajectory with python?
I am attempting to analyse the radial distribution function (oxygen to oxygen) for a ~400ps simulation on a droplet of water (MD done with NAMD). I am using the python library MDAnalysis to do this. ...
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Molecular dynamics frame distorted by VMD?
I am running a VMD renderer to view my GROMACS molecular dynamics output.
At one frame, the geometry looks fairly normal like this:
At another frame, it displays a distorted geometry, with the ...
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Can I compute the free energy difference in (temporally) nearby micro-states using the Zwanzig equation for Free Energy Perturbation?
I wanted to understand the Free Energy Perturbation in an NVT ensemble.
Wikipedia explains it as:
$$
\tag{1}
\Delta F = F_1 - F_0 = -\kappa T \ln \left<\exp\left( \frac{-(E_1-E_0)}{\kappa T}\right)...
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How to calculate the computational time required for a MD simulation
I have a ligand and receptor to simulate with MD. These are my specs:
Receptor has 4674 atoms,
Ligand has 273 atoms
CHARMM force field
MD software GROMACS
Computing machine: Amazon g4dn.xlarge (1 GPU ...
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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 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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Large pressure fluctuations in molecular dynamics
I'm performing MD simulations, using NPT ensemble. The problem is that the pressure fluctuates severely and doesn't average at required level.
For example, I set the pressure at 1 bar and it averages ...
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How do I build and run a simulation of water molecules in NAMD?
So, I have started to learn NAMD because I need that for a project I will be doing in the next couple of months. I have some prior experience of MD with gromacs. I thought that since NAMD has a GUI ...
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Which equation makes it possible to calculate the forces of attraction between a surface and molecules?
Which equation makes it possible to calculate the forces of attraction between a surface and molecules? Is there any free software that implements such a calculation?
[Clarification 1] Between a ...
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Langevin vs Nosé–Hoover thermostat
can anyone explain the pros and cons of using the Langevin vs Nosé–Hoover thermostat? I wonder how to choose a suitable thermostat for a system, such as oxide, organic materials.
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Is it possible to build a force field that suits all elements based on VASP's machine learning result?
I have tried to use VASP's machine learning force field calculation during running molecular dynamics simulation with a supercell including some elements of Ti, O, Cu, etc. It does increase the speed ...
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How to visualize protein-ligand complex MD run using VMD
GROMACS version: gmx, version 2021.4
GROMACS modification: No
I'm following the Protein-Ligand Complex tutorial.
I'd like to visualize the binding using VMD.
I use the output from these commands:
<...
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Basics of configuration initialization strategies used in molecular dynamics? [duplicate]
This answer to Basics of numerical energy minimization techniques used in molecular dynamics? mentions
conjugate gradients, BFGS for energy minimization
and
Metropolis Monte Carlo (and the) the ...
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How to apply FIRE to many atoms where P=F·v seems to be a vector rather than a scalar?
Introduction/Preamble
@SusiLehtola's answer to Basics of numerical energy minimization techniques used in molecular dynamics? mentions conjugate gradients, BFGS for energy minimization, Metropolis ...
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Are MD and MC both able to study both equilibrium and non-equilibrium systems?
As far as I understand, a system in equilibrium is which already reached its equilibrium state. And, a non-equilibrium system is which hasn't reached its equilibrium state yet.
Are MD (Molecular ...
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