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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2answers
88 views

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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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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1answer
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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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1answer
74 views

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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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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0answers
34 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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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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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 ...
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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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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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1answer
77 views

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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4answers
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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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2answers
394 views

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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41 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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1answer
35 views

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
197 views

How to compute the number of ATP molecules that can be produced from breaking down an unsaturated free fatty acid?

From studying $\beta$-oxidation of free fatty acids, I've learned how to compute for the ATP equivalence of even-chain and odd-chain free fatty acids. What really bothers me now is how to compute for ...
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0answers
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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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2answers
84 views

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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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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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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0answers
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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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1answer
105 views

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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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 ...
6
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1answer
102 views

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 ...
3
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1answer
83 views

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 ...
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 ...
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31 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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1answer
162 views

What causes energy peaks during a molecular dynamics energy minimization?

I'm minimizing the energy of a protein with NAMD using the fixedatom feature. I put my protein in a water box, and I allow all atoms other than the protein backbone ...
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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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1answer
61 views

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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1answer
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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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1answer
50 views

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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222 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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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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1answer
45 views

Molecular dynamics after modeling a protein loop. Necessary?

Firstly, I am postign this question to both chemistry and physics stacks exchange as I am not sure to which it belongs and to use the benefits from both sites. I have modeled missing loops in a PDB ...
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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 ...
4
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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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0answers
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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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1answer
527 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? ...
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1answer
63 views

How to calculate size of a specific cavity in a protein for every frame in trajectory file?

Here is the situation, I have trajecory file of a protein of interest. That protein has 2 main cavities that are participating in interraction with ligands or other proteins and also other cavities. ...
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0answers
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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 ...
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1answer
131 views

Question About Reversible Reactions and Batteries

So my book says that the batteries we have considered so far( Daniell cells) are low life span, because they reach equilibrium too fast. In the next paragraph, it says they are also made by ...
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1answer
198 views

Molecular dynamics (Mac OSX user): what software can I use to plot RDFs for NPT simulations? VMD only works for NVT (constant volume)

I would be very grateful if someone could recommend a way to plot RDFs for NPT ensemble molecular dynamics simulation results. I use CP2K to run NVT simulations and usually use VMD to process ...
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367 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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1answer
136 views

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 ...
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1answer
121 views

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 ...