# 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 ...
1 vote
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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 ...
1 vote
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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. ...
1 vote
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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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1 vote
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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 ...
1 vote
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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, ...
1 vote
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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 ...
1 vote
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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 ...
1 vote
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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 ...
1 vote
104 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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### 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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### 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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### 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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