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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When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?
Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled ...
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OOM Error Calculating ESP Charges with Psi4
I'm trying to create a script to generate partial charges for a given .dat file.
As an example of my process, I'm currently using gromacs to run minimization on a box of propane. It outputs a min.gro ...
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Why having a carbonyl group is not contributing to binding energy
I am carrying out a virtual screening project for a protein receptor to identify possible ligands (small molecules). After the virtual screening, molecular dynamics, and MMGBSA calculation, I ...
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EM Induction from Diffusing Ionic Wave Front
I am studying the Belousov-Zhabotinsky Reaction-Diffusion system in ~1mm wide 1-dimensional channels. In my research we are activating the reduced phase with a silver wire and studying the propagation ...
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The need for accurcy in constrained molecular dynamics simulations
In constrained molecular dynamics a system of differential algebraic equations
$$\begin{align} \dot{q} &= v, \\ M\dot{v} & = f(q) - G(q)^T \lambda, \\ g(q) &= 0 \end{align} $$
is solved. ...
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Ratio between the corresponding force constants of Cl2 and F2
MCQ Question:
Vibrational frequency (f) of a diatomic molecule is given by
where 𝑘 is the force constant and 𝜇 is the reduced mass. For a diatomic molecule (AX), the reduce mass is given by
where �...
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Why does a symmetric stretch mode not have an imaginary frequency?
Currently studying potential energy systems and our professor asked a question at the end of a lecture and I can't wrap my head around it.
He said, "Picture a 2D PES for the simple reaction of H+...
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Software for running dynamics simulation of polymeric and mixed biomaterial (e.g hydrogels)
I was working on the development of a soft solid hydrogel having polymeric chains and molecules of different compounds dissolved in Phosphate Buffered Saline solution. There is a sub-study regarding ...
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Resource estimate for ab initio calculation [closed]
I have recently come across this very intriguing paper “The Fundamental Vibration of Molecular Hydrogen”.
I have asked the authors the following naïve questions directly via email?
What was the ...
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Van der Waals Parameters (non-bonded parameter) in Amber? [duplicate]
I have a complex that contains transition metals. I am doing parametrization and building the force field.
I have one question about the frcmod file.
In the file,
...
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Crystal packing prediction for simple organic molecules?
Is it yet possible to predict a simple organic molecule's crystal structure or how the molecules arrange in a crystal without diffraction measurements?
By crystal structure I mean, how would molecules ...
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Schrodinger operator with matrix potential and Green's function
Clearly Schrodinger operators with matrix potentials appear very naturally in molecular dynamics/quantum chemistry, particularly when considering a crude adiabatic basis or diabatic basis for an ...
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Charge polarisation in acetamide molecule due to different lithium salts (varying anions)
I am trying to understand how will acetamide molecules behave in the presence of lithium salts with different anions (nitrate, bromide and perchlorate).
Among the three, it is evident that bromide is ...
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Practical use of the partition function in molecular simulations
In the second chapter of Understanding Molecular Simulation, Frenkel and Smit derive an equation for the partition function and the thermal average of the generic observable A, stating that these ...
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Vibrations of metal complexes (polyatomic molecules)
I am reading about vibrational spectroscopy of polyatomic molecules and specifically about metal complexes. What I don't understand is what happens on the vibrational modes of the ligand (e.g. water) ...
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Eigenenergies and states of Jahn–Teller molecule
I'm generally interested in numerical chemistry. In our lecture, we have discussed the $E \otimes e$ Jahn–Teller molecule with the following Hamiltonian
\begin{align}
H = \epsilon n_d + \omega ( a^{\...
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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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Kinetic energy of liquid [closed]
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 ...
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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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Ordered and random energy [closed]
One of the books refer to potential energy being ordered whereas heat energy being random. Could someone explain what is ordered and random energy?
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What is the most appropriate (and easy-to-use) all-atoms force field for liquid electrolytes?
I need to simulate a salt diluted in a liquid electrolyte.
My experience is with LAMMPS, but so far I only had coarse grained toy models, and setting up the force field was straightforward.
Now I have ...
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Dielectric polarization: how to identify what part of the total polarization (dipolar+electronic+ionic) I need (conceptual question, I use DFPT, VASP)
I am doing polarization calculations to get data for use in other calculations. To start with, I want to calculate the static dielectric constant. However, I'm a newbie to polarization and it is a ...
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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 ...
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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:
$$U_{\mathrm{dihedral}} = \begin{cases}
k(1+\cos (n\psi + \phi)),&...
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How much should I scan an aromatic dihedral?
Suppose I have a napthalene-like molecule (attached), and I would like to scan (relaxed) its aromatic dihedral (highlighted atoms). I used CGENFF to obtain its dihedral parameters as follows,
HGA4 ...
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Molecular dynamics simulation of a protein in acidic medium
I want to perform an MD simulation of a protein under acidic solvent conditions. A quick literature search seems to indicate that people are more interested in the protonation of protein side chains (...
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How are class II force field cross-terms derived?
In some class II force fields, there are cross-terms that characterize bond-bond, bond-angle interactions and others. Example of equations below:
$$\sum_{bond-bond}^{}k_{bb}(b-b_{0})(b^{'}-b^{'}_{0})$$...
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How can I build the wyoming like montmorillonite unit cell in avogadro for a molecular dynamics simulation?
I am trying to build a unit cell for Wyoming-like montmorillonite, using Avogadro software. I am not sure how can I get access to the atom coordination and how to generate the .xyz file at the end? Is ...
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Software to perform molecular dynamic simulation
I have got aggregate of 4 non-protein compounds I would submit for molecular dynamics simulation. The problem is I can't find software capable to do that. Amber, GROMACS, LAMMPS, all of them require ...
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Calculating self-diffusion coefficient from MSD programmatically
According to the Einstein relationship, the diffusion coefficient $D$ is
$$\lim _{t\rightarrow \infty} \frac{\langle \left(\mathbf{r}(t)-\mathbf{r}(0) \right) ^2\rangle}{6t} = D$$
I have run a MD ...
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Potential energy difference with different force fields
I am modeling a simple 2D Graphitic Carbon Nitride (g-C3N4) nanosheet with 54 atoms. I used several force fields with both LAMMPS and GROMACS and the potential energies of the system in npt at 1K and ...
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I calculated internal energy at various temperatures and pressures. My results differ from someone else's. Is this OK?
I would like to make sure that my understanding of internal energy is correct. I'm not a thermodynamicist, so apologies in advance for what is probably a basic question.
I previously calculated ...
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Solving the Schrödinger equation for a rotating triatomic linear molecule
This source is showing that solving the Schrödinger equation for a triatmoic linear molecule yields the same formula for the rotationaI quantum states $BJ(J+1)$ as for dipoles.
For dipoles, the total ...
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Relationship between reaction quotient and potential energy [closed]
I am trying to calculate the Gibbs free energy in an NVT simulation. Although
$$\Delta G = -RT\ln Q,$$
in my simulation I can't calculate
$$Q = \frac{[\text{Products}]}{[\text{Reactants}]}$$
because I ...
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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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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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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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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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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 ...
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How can the torsional barrier of a polymer determined by molecular dynamics?
First consider a simple polymer, like polyacetylene:
Its torsional barrier can be determined by DFT calculations by considering "enough" units and performing a simple dihedral scan. "Enough" appears ...
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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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Pressure of a system of particles
I'll derive the pressure of a system of particles, which would be used in a MD simulation for example, according to Allen's Computer Simulation of Liquids and show where my issue is.
Consider a ...
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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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Fixing incongruities in PES Scan [closed]
I tried to parameterize a particular x-y-z-t dihedral angle of novel molecule using a Quantum Mechanical scan, but I got the strange result below.
The energy changes sharply around 130° and $E_\text{...
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Help with molecular dynamics and computational modelling to check validity of hypothesis regarding SN2 reaction mechanisms [closed]
Polar aprotic solvents have a less hindered electronegative atom pointing out, namely oxygen, fluorine, and nitrogen, all of which have lone pairs besides having a partial negative charge. Now, all ...
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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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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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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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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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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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