Molecular dynamics is a method in computational chemistry that is used to study the movement of atoms and molecules.
Questions tagged [molecular-dynamics]
102 questions
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How did Noe et al. derive $k_{AB}$ in their PNAS 2009 paper?
This question is regarding Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations which uses Markov State Model to find the equilibrium protein folding pathways from off-equilibrium simulations.
I find the…
0x90
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Why do the peaks in a radial distribution function graph have a probability >1
Why do RDF plots have the probability at a particular distance >1. How can probability be more than one?
I am asking this because I want to understand what do the peaks of different length but at the same position on the x axis mean
The below is an…
fireball.1
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Calculate collision density of air
Caluculate the collision density between $\ce{O2}$ and $\ce{N2}$ in air at $T = \pu{10 ^\circ C}$. Assume that the air is an ideal gas and that the molecules are spheres with diameters $\pu{0.36 nm}$ for $\ce{O2}$ and $\pu{0.37 nm}$ for $\ce{N2}$.…
confused
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How to extract force when the center of mass of molecules is put in the box in GROMACS?
To extract the force as in the title I used the gmx trjconv command like below.
gmx trjconv -f alad.trr -s alad.tpr -n alad.ndx -pbc mol -novel -force -o alad.gro
However, the force was not extracted in alad.gro file.
Of course, I got the…
Yeonju
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How can I build the wyoming like montmorillonite unit cell in avogadro for a molecular dynamics simulation?
I am trying to build a unit cell for Wyoming-like montmorillonite, using Avogadro software. I am not sure how can I get access to the atom coordination and how to generate the .xyz file at the end? Is there any file that I can use as guidance during…
mah6iid
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Potential energy difference with different force fields
I am modeling a simple 2D Graphitic Carbon Nitride (g-C3N4) nanosheet with 54 atoms. I used several force fields with both LAMMPS and GROMACS and the potential energies of the system in npt at 1K and 1 atmosphere are:
LAMMPS using…
Ehsan Shahini
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Courses for Molecular Modeling?
I'm probably doing overkill trying to learn a bit of everything, but here's my story. I have a B.S. in Math with a minor in Microbiology, and I'm currently taking Computer Science courses online to meet the pre-requisites for a Master's in CS where…
Bryan Aardvark
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Constructing potential energy surface of a periodic system, how to deal with atoms moving out of the supercell?
I'm using NVE ensemble for doing molecular dynamics (MD) simulations. The periodic system I'm working with contains $50$ atoms and the "calculator" for calculating potential energies and forces is a trained neural network. The platform I'm using for…
meTchaikovsky
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Kinetic energy of liquid
Does intermolecular force of attraction have anything to do with molecules having more energy in their liquid state than their solid state? If not, what is responsible for greater kinetic energy in liquids?
Lime
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