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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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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370 views

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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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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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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142 views

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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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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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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237 views

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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86 views

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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168 views

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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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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47 views

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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42 views

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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41 views

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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52 views

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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56 views

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 ...
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How to Scan Aromatic Dihedrals To Obtain Force Field Parameters

I am trying to generate new force field parameters based on quantum mechanical calculation. I used amber manual "parameter development" title for this and I calculated bond-angle-non bond parameters ...
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214 views

Amber Force Field Improper Parameterization Huge Kb Problem

I am trying to parameterize a molecule. I know dihedrals and impropers are the same for Amber Force Field. (Source: http://archive.ambermd.org/201004/0334.html) So, I did PET scan for improper and I ...
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239 views

How to develop a Reactive Force Field (ReaxFF)? (Molecular simulation)

Currently, I am working on CO2 capture on Hydrotalcites as solid adsorbents. I want to run molecular simulations to analyse the behaviour of the material under different temperatures, pressures and ...
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208 views

Generalized reaction rate and derivation

Most textbooks give the reaction rate $$r = k C_\ce{A}^a C_\ce{B}^b \tag{1}$$ for the elementary process $\ce{a A + b B -> P}$. However, expression (1) is not valid in the general case: e.g. it ...
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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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43 views

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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27 views

Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance

I am new to molecular simulation, so please excuse what is likely a very silly question. I am using the python package openmmtools to run a simple molecular simulation problem using the metropolis ...
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26 views

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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26 views

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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20 views

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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46 views

Is the 12-6 Lennard Jones potential a good description of van der Waals interaction energy?

It seems to me that the Lennard Jones potential oversimplifies the more complex nature of van der Waals forces. However, in most of the MD simulation package, this is generally accepted.
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107 views

Calculating the free energy of separation in AMBER

I am currently busy with my master's research project and I'm trying to calculate the free energy of separation of two cellobiose molecules in ionic liquid, that is, calculate the free energy of ...
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65 views

PTFE-to-PTFE or PTFE-to-Copper pressure seal

I am currently working on an engineering project with a friend. Without giving too much away, I have two parallel strips of Zirconium-Copper alloy sandwiched between an upper and lower piece of smooth ...
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33 views

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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33 views

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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54 views

How can I define a torsion force field for $n$ points in space?

I would like to define a model for torsion force field between $n$ point in space. I thought to generalize the OPLS model: $$ \sum_\mathrm{dihedrals} \left( \frac {V_1} {2} \left [ 1 + \cos (\phi-\...
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53 views

What is "time-dependent evolution of the complex noncovalent interaction networks" and why this is important?

From Maximilian Scheurer, Peter Rodenkirch, Marc Siggel, Rafael C. Bernardi, Klaus Schulten, Emad Tajkhorshid and Till Rudack Biophysical Journal, Volume 114, Issue 3, 577-583: One of the most ...
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535 views

Using AutoDock Vina to dock multiple ligands to multiple receptors?

I am trying do that what the title depicts, but I keep running into errors creating the executable script. Is it even possible to automate the docking of multiple ligands to multiple receptors? ...