What is Molecular dynamics: Definition and 44 Discussions
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanics force fields. The method is applied mostly in chemical physics, materials science, and biophysics.
Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in numerical integration that can be minimized with proper selection of algorithms and parameters, but not eliminated entirely.
For systems that obey the ergodic hypothesis, the evolution of one molecular dynamics simulation may be used to determine macroscopic thermodynamic properties of the system: the time averages of an ergodic system correspond to microcanonical ensemble averages. MD has also been termed "statistical mechanics by numbers" and "Laplace's vision of Newtonian mechanics" of predicting the future by animating nature's forces and allowing insight into molecular motion on an atomic scale.
TL;DR Summary: Briefly i'm asking for guidance through self-studying biophysics.
Hello everyone, i've almost finished my bsc in physics and i got intrigued by biophysics, although my university doesn't provide courses for the subject. I wanted to get a grasp of the subject by myself but...
I am trying to analyse the dynamics of a cluster of 79 atoms.
The system can be described with:
##\omega^2 \vec x = \tilde D\vec x##
Where ##\omega^2## (the eigenvalues) are the squares of the vibration frequencies for each mode of motion, ##\tilde D## is the "dynamical matrix" which is a...
I am currently reading this [paper by Noid et. al.](https://doi.org/10.1063/1.2938860) on the rigorous bridge between atomistic and coarse-grained simulations.
In the paper, he defined a linear map from the atomistic coordinates and momenta $$\mathbf{r}^n, \mathbf{p}^n$$ to the coarse-grained...
I want to create multiple molecular dynamics simulations using LAMMPS which are different only in the initial velocity of the atoms. LAMMPS allows you to use a random seed to generate an initial velocity. I plan to just use successive numbers, so if there are 5 simulations, the seeds would be...
Hi. For some background, I am running molecular dynamics simulations of silica fracture in LAMMPS. Each point represents the location of a broken bond. I would like to find regions where many bonds are breaking, which I speculate would be locations of crack formation. These computations are...
In molecular dynamics people use periodic boundaries to confine particles being simulated. I read here that they are used to simulate large "infinite" particle systems. How can I know that the periodic boundary is simulating actual molecular outcomes for a finite particle system that had a large...
I am interested in showing a visualization of water molecules in a time-varying electric/magnetic field as part of my PhD work.
I would like something like this visualization:
, but with an external time-varying field applied.
At first, I thought of simply animating water molecules...
Following Frekel-Smit book: https://www.amazon.it/dp/0122673514/
I am trying to write a program based on the algorithms 3,4,5 and 6 in the book.
I use a cutted-shifted Lennard Jones potential, with cutoff radius at 2σ.
#include <iostream>
#include <cstdlib>
#include <cmath>
#include<fstream>...
Homework Statement
I am working on a MD code (http://www.acmm.nl/molsim/frenkel_smit/Exercise_10/index.html) which uses the position Verlet algorithm to integrate the equations of motion and a velocity rescaling algorithm for initialization in periodic boundary conditions.
I wondered why...
What is the exact difference between energy minimization and equilibration in a molecular dynamics simulation since both brings the system to the local energy minima?
Hi all,
I'm doing a bit of material science research at my university. I'm running molecular dynamics simulation programs like Lammps and Amber as part of it, and I'm pretty new to the whole thing (just like I'm pretty new to this forum). I'd like to ask, has anyone here used Amber to find their...
Dear all,
I am using molecular dynamics to calculate energy for ionic liquid. In the article that is proposed equation of state that I want to use, the author would call the energy in the following formula(u) conformational(potential energy):
(du/dv)T + T(dp/dT)V = ptot
Firt T and V are...
Dear all,
I've been working on an ionic liquid that I was involved in simulating with Lammps, but when I started to write its paper, I found a mistake (or a neglect) that makes almost all the results useless. I would always compare the pVT simulation data with the corresponding experimental data...
Integral constant for internal energy of ionic liquid
I have a question, and I will be really grateful if someone helps me. I have a polynomial equation for internal energy which I calculated by integration an equation of state formula, which is based on density. But, because I calculated this...
Hi,
I'm working on a project using LAMMPS. I am very new to the software and find the documentation doesn't always answer the fundamental questions I have. I noted previous LAMMPS queries were posted on this forum, although I am from a mechanical/materials engineering background.
I am trying...
Hi All,
What are the main differences between statistical and dynamics properties in physics? Could you please explain the difference for problems in both classical and quantum mechanics. For instance, path integral molecular dynamics is supposed to give statistical properties of a quantum...
In my rough understanding Molecular Dynamics using Classical Newtonian mechanics is a 6N dimensional non linear system. 6N dimension because you have 3 position vectors and 3 momentum vectors for each N particles. Nonlinearity because of the terms in force fields. In principle this system can...
Hello everyone, I'm a graduate student in a biophysics lab. I'm trying to run a QM/MM simulation with a protein that binds 3 Ca2+ ions, and as such I am having a devil of a time getting the SCF to converge. I've tried DIIS, KDIIS, damping, and a few other methods to try to get convergence with...
Hi, does anyone know of an easy way to calculate the error in <x^2> from the error in <x>? I am running a molecular dynamics simulation and trying to work out the error in the fluctuation of kinetic energy <dEk> = <3/2NT^2> - <3/2NT>^2 from the error in <T>.
Thanks in advance
Consider the image below
Does it emit all 3 types of heat in the form of UV, IR and light?
At what threshold does light start to appear and what colors should it illuminate?
Hypothetically, say I have an induction furnace and is capable of setting frequencies to about 700THz, will it be able to...
I have nine sets of data with x,y coords that are the position of a particle. I can ListPlot the particle positions on a single plot, but, I want to animate this.
ListPlot[{mydata1, mydata2, mydata3, mydata4, mydata5, mydata6, mydata7, mydata8, mydata9}, PlotRange -> {{-1, 20}, {-1, 20}}]
I...
Hey,
When performing Molecular dynamic or Monte Carlo simulation (in NPT or NVT ensemble), I'm wondering whether there is any difference between the average energy of the system and the energy of the average structure.
If there is a difference, how munch should it be? and why?
Does the the...
I am trying to understand Bernoullis from Newton laws applied to molecular dynamics (as opposed to conservation laws)
From the conservation laws I understand for a incompressible invicous (experiencing no friction effects ) Ideal fluid
Mass is neither created nor destroyed Mass in = Mass...
Just joined. I've been slowly working my way through Susskind's Theoretical Minimum books, so I'll be looking for discussions of those and his lectures on the same topics.
I have a lot of scientific interests, including fundamental physics, mathematical biology, economic geology, electronics...
I am unable to prove step 8.3 in this proof of the path integral formulation of molecular dynamics
https://files.nyu.edu/mt33/public/jpc_feat/node11.html
Any help would be much appreciated.
Homework Statement
The Lennard-Jones potential function u(r) = 4ε[(σ/r)^12 - (σ/r)^6]
If intermolecular interactions are ignored in this calculation for r > rc , show that in the mean field approximation in the long range correction [itex] P*LR to the measured pressure is given by...
Hello everyone.
I'm am looking for some literature (articles or books) containing information about how is the relation between the liquid water pressure (macroscopic thermodynamic quantity) and it's quantum molecular dynamics (collisions, vibrations, etc.). Like: The pressure increase...
Hello everyone!
I have constructed a model of a silicon crystal, consisting of 64 atoms, for my various needs of testing physical phenomena in that substance(Silicon).
At present, rather annoyingly, I am still stuck at the basic operational level, that is, calibrating the system to an expected...
Hi All,
I'm trying to write some "wrapper" software that uses forces calculated from a quantum mechanical potential (ie. Hartree-Fock, DFT, etc.) to evolve a system according to classical Newtonian mechanics (ignoring any periodic boundary conditions, etc.). I believe I have successfully coded...
Hey,
I've simulated a solid metal cluster of gold fcc100
And a surface Platinum in fcc111 using a classical mechanical approach.
Do you think i could get the surface free energies(the ones to use in determining the Wulff shape) from periodic boundary conditions and if so how? I am really...
Hi,
Say you have a simulation of a nano particle resting on a flat surface of metals. It is described by the effective medium theory. How do you find the free energy of a face to be used in the Wulff construction. A suggestion i got was to use periodic boundary conditions in all directions...
I'm building a code for Molecular dynamics (in C).
I'm employing Lennard Jones Potential, periodic border conditions and I integrate Newton's equations by making use of Verlet Integration.
When I plot Time vs Energy graph, what I get isn't a constant! but when border condition are remove, then...
What would be a rough estimate of the computational complexity to simulate an embryo in a full-atom scale from the instant of conception to the death of the aging adult?
Its a purely theoretical question and I know that its something like daydreaming for the current technology, but I would...
Hello,
I am doing my undergraduate in the dept of 'mechanical design of intelligent systems' in Japan. During the fourth year we don't have any lectures and just work on research and our thesis. My field of research for the whole year will be molecular dynamics. Although this field uses...
Guys,
The question is as follows:
Q) I currently simulate organic systems using the Molecular Dynamics (MD) program. Previously, I have used MD to simulate primarily Silicon and Boron interaction at relatively high energies which is fine with the classical approach used with MD. I was...
Dear all,
I am not sure if this is the right place to ask the following. (Moderators, please move this thread to the right sub-forum if necessary.)
The question I am having is related to molecular dynamics. In the book "Molecular Dynamics Simulation: Elementary Methods" by J. M. Haile, a...
I get this formula in a MD paper:Wavelet-based multi-scale coarse graining approach for DNA molecules
P(d)=A*exp(-U(d)/kT)
P(d) is the distribution function, U(d) is the potentital.
How does this formula come?
In the paper I read about this, they get the distribution first, and obtain the...
I have a possibility to simulate Molecular dynamics (MD). I want to find someone who need it. I propose to simulate ab initio quantum mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The interaction between ions and electrons is described using ultrasoft...
Hi ;
Is there anybody using SageMD for molecular experiments. I am planning to set up a mail group for SageMD or all the molecular dynamics simulator software. Please write me if you want to join or if you know any other place for me to find anyone please tell me... Thank you all...
How different/similar is molecular dynamics from rigid body dynamics? Could I use RBD software such as ODE to simulate MD? What assumptions/modifications would I need to make for this to work (e.g. treat atoms as rigid spheres connected through some special type of joints)?