Questions tagged [molecular-dynamics]
Molecular dynamics is a method in computational chemistry that is used to study the movement of atoms and molecules.
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Why are MD (Molecular Dynamics) simulations performed at room temperature for the purposes of studying proteins?
All of the MD simulations which are cited in the literature seem to be performed at room temperature (~300 Kelvins), while enzymes are usually bioactive at body temperature (~310 Kelvins).
I am ...
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Why aren't the Anton computers used more widely?
The Anton computers are purpose-built by DE Shaw research for molecular dynamics simulations. They achieve performance up to an order of magnitude faster than can be achieved with commodity hardware, ...
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Boltzmann Distribution in Molecular Dynamics Simulation?
The Boltzmann distribution is often used to describe the population of energy states at different temperatures, i.e. something like
$$\dfrac{g_i}{g_j} = \mathrm{exp}\left(-(E_i-E_j)\times \frac{1}{...
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In a molecular dynamics context, is the methyl rotation in propene a symmetric or asymmetric internal rotor?
In a prior question, I asked about the (a)symmetry of the potential energy surface of the methyl rotation of propene. In that context, the kinetic energy of the nuclear motions is of course assumed ...
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Is it true that an evaporating molecule has the same kinetic energy as a molecule in a pot of boiling water?
A molecule on the surface of room-temperature water shoots off the surface of said water, or in other words, it "evaporates." It does so because it gained kinetic energy ${x}$, and ${x}$ was great ...
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How to perform molecular dynamics simulations of charged systems?
The GROMACS official documentation (see here) states that a system with non-zero total charge will yield an error:
System has non-zero total charge
Notifies you that counter-ions may be required for ...
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1answer
791 views
How to simulate phase separation in a discrete system using LAMMPS?
I would like to simulate phase separation in LAMMPS and need advice what kind of two particle systems and interactions will yield phase separation.
For example, a meta stable phase separation is ...
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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 ...
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Cloud-based molecular modeling software
I’m an IT Acquisitions and Licensing specialist researching well-supported cloud software alternatives to Fujitsu’s molecular modeling SCiGRESS. I am coming in with a tech background, but little to ...
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1answer
995 views
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 ...
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1answer
408 views
How to write an entire trajectory into a single PDB file?
I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library.
With VMD if I do ...
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1answer
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Vibrational state dependency of the reaction cross section
I'm reading p.1238 of Mcquarrie's Physical Chemistry: A Molecular Approach textbook.
In the last line of the page, the author explains that the value of the reaction cross section in the constant ...
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Force Constants for Angles From Gaussian To AMBER: which value should I put in the matrix equation?
I am trying to make a new force field in AMBER for a novel compound including boron (which does not exist in GAFF). For this, I calculated freq and I found bond force constants but I couldn't find ...
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1answer
81 views
What types of energies can be determined by molecular dynamics in gas phase or explicit solvents?
For molecular dynamics in the gas phase I've seen that electronic energy can be determined and also decomposed in kinetic and potential energy. I've also seen that we can include ZPE. But can we ...
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Solving the Schrödinger equation for a rotating triatomic linear molecule
This source is showing that solving the Schrödinger equation for a triatmoic linear molecule yields the same formula for the rotationaI quantum states $BJ(J+1)$ as for dipoles.
For dipoles, the total ...
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Why the use of MD simulations is less popular for the study of carbohydrates?
In classical all-atom MD simulations, the force fields for proteins, nucleic acids and lipids seem to be more well developed than carbohydrates. It seems to me that the use of MD simulations is not so ...
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SARS-CoV - relative size of the spike protein
I am taking an online course in image analysis and have been asked to use the attached image to determine the size of the SARS-S protein of the SARS-CoV relative to the total of its proteins. However, ...
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Building an average model from MD snapshots
I am performing a molecular dynamics simulation, and I am taking "snapshots" of the system at regular intervals.
The aim is that of finding the preferred geometry of a molecule in solution.
Are you ...
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1answer
122 views
Tools for Molecular Simulation
I am a high school student and I don't know a whole lot about molecular simulation. I wish to view different conformers of cyclohexane and the changes that occur when substituents are attached (for ...
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1answer
342 views
Hessian Matrix and Physical directions: Potential Energy Surface
How do the eigenvectors of the Hessian Matrix for potential energy surface correspond directly to the physical directions of translation, rotation and vibration?
I see that they might correspond to ...
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1answer
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Would there be need for periodic DFT if we are able to get all the forcefields of all the elements in the periodic table in ReaxFF?
Since ReaxFF combines the advantages of DFT and Classical MD, would there be any need for periodic DFT calculations if we can have all the forcefields of all the elements of all the possible systems?
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Keeping the electronic configuration in the ground state is expensive in Ab-initio MD?
In E. Sandré & A. Pasturel's An Introduction to Ab-Initio Molecular Dynamics Schemes
If using small time steps (typically in the order of a few tenth of femto-second), the changes in the ...
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What is the “curse of dimensionality” in molecular dynamics?
The 'curse of dimensionality' or the 'bottleneck problem' in molecular dynamics is explained in page 5 and 6 of Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods by Dominic Marx and Jurg ...
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Computing optimized 3D structures in python that take solvent into account
I have been using RDKit to generate 3D coordinates, cleaning-up the structures using a general-purpose force field as follows:
...
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What computational methods are available for predicting nanoparticle structure?
I'm a quantum chemist, and nearly every system I've ever cared about has been studied by DFT. However, I am currently trying to model the surface interactions on a nanoparticle around 100 nm in ...
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LAMMPS: MD simulation of molecules? [closed]
I need to do molecular dynamics simulation of cyclodextrine molecules for a project and I am searching for an open source solution that can be used. I found LAMMPS to be quite well maintained and ...
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1answer
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How much time for a water molecule in pure water to reach the top of a glass of water?
I have a curiosity to know how long it will take for a water molecule to move a certain distance in pure water. I can put it simply as how much time for a water molecule to travel the whole length of ...
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1answer
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Is there a known relation between the diffusion of a molecule and the diffusion of the reactants?
I have a plasma consisting of elements A and B (which have a similar mass). These elements can react to form molecules AB.
$$
\ce{A + B -> AB}
$$
Now if my plasma or gas is expanding based on ...
3
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1answer
59 views
Determining the torsion energy profile of butadiene by molecular dynamics
Disclaimer: this question is related to my previous question, although it is much more detailed
Consider the following rotation of butadiene:
I want to determine the relative energy of each dihedral ...
3
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1answer
64 views
How to extract force when the center of mass of molecules is put in the box in GROMACS?
To extract the force as in the title I used the gmx trjconv command like below.
...
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1answer
414 views
How can you simulate the effect of a solvent on a polymer in an MD simulation?
I'm doing a molecular dynamics simulation of polymer melts and I want to include the effect of a good/bad solvent on the melt. How can this be done?
My simulation models polymers using a bead-spring ...
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Can someone help me understand the motivation behind and visualize the dihedral potential and the Urey-Bradley potential?
I am studying statistical mechanics and force-fields, and I see a lot of this formula being thrown around with no explanation:
$$U_{\mathrm{dihedral}} = \begin{cases}
k(1+\cos (n\psi + \phi)),&...
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Normal Mode Analysis of proteins
I'm trying to do Normal Mode Analysis for my MD trajectory. I'm following Amber tutorial (http://ambermd.org/tutorials/advanced/tutorial3/py_script/section5.htm) which uses an example of estrogen ...
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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 $\pu{0.36 nm}$ ...
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Simple sandbox software for an interactive molecular dynamics simulation
I'm not sure if this is the right site to ask a such question. But I'm getting to learn the world of the small.
I know there is software out there like NAMD, and LAMMPS. But these tools are very ...
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Minimum image convention and the atom “seeing” itself
The minimum image convention in molecular dynamics can be stated as:
A particle in the central square must not interact with one of its neighbors in the central square and an image of this neighbor ...
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1answer
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Calculate force on atoms given the energy of configuration, trajectory of simulation and position of atoms in each frame
Background
I am using a neural network to calculate the potential energy of atoms in a configuration and then adding energy of all atoms to compare it with the true energy of the configuration(label) ...
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1answer
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Calculation of free energy from potential and kinetic energy
I am having trouble understanding how (and even whether it's possible) to get free energy from kinetic and potential energy.
I have run molecular dynamics simulations (NPT ensemble, CP2K software), ...
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2answers
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Question during radius of gyration calculation from XYZ trajectoris of atoms
I have molecular dynamic simulation result of 100 polymer molecules (liquid), and I'm trying to calculate the radius of gyration using atomistic mass, molecular mass, and xyz coordinate of atoms. I'm ...
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1answer
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Understanding water models?
I generally work on fluid flow, so some basic concepts in chemistry are new to me.
Work I'm doing requires use of molecular dynamics (MD) to do classical potential simulations of water–NaCl systems ...
2
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1answer
91 views
Magnitude of Lennard-Jones force evaluated with molecular dynamics simulation
The intent is to evaluate the error source of a molecular dynamics (MD) simulation which is only based on the Lennard-Jones interaction between noble gases (helium in this case). What is the magnitude ...
2
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1answer
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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 ...
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1answer
751 views
Radial pair distribution function (VMD). How to define it for a water NaCl system with multiple Na and Cl?
I'm struggling to understand a paper in which someone has presented radial distribution functions (RDFs) for a system that contains multiple Na, Cl, and water atoms/molecules. I don't know exactly ...
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1answer
242 views
Courses for Molecular Modeling? [closed]
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 ...
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0answers
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How to model a molecule of benzene surrounded by 100 molecules of water with molecular dynamics?
I have experience calculating molecular properties (mostly DFT). However, I would like to spend some time on molecular dynamics methods. I would like to ask your advice to direct me towards a program ...
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Molecular dynamics simulation of a protein in acidic medium
I want to perform an MD simulation of a protein under acidic solvent conditions. A quick literature search seems to indicate that people are more interested in the protonation of protein side chains (...
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How are class II force field cross-terms derived?
In some class II force fields, there are cross-terms that characterize bond-bond, bond-angle interactions and others. Example of equations below:
$$\sum_{bond-bond}^{}k_{bb}(b-b_{0})(b^{'}-b^{'}_{0})$$...
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Relationship between reaction quotient and potential energy [closed]
I am trying to calculate the Gibbs free energy in an NVT simulation. Although
$$\Delta G = -RT\ln Q,$$
in my simulation I can't calculate
$$Q = \frac{[\text{Products}]}{[\text{Reactants}]}$$
because I ...
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0answers
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Difference between docking and scoring?
I'm taking an undergraduate level class on computer based drug design. The class is more for biology students than people with a strong understanding in physics and computer science.
With that said,...
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Do I understand correctly that simulation volume influences relative permittivity calculations? If so, how is the result useful?
I am having a lot of trouble understanding the influence of volume on relative permittivity/static dielectric constant. I'm not a chemist, but am using molecular dynamics to calculate relative ...
