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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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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1answer
607 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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51 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 ...
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1answer
58 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 ...
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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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51 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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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
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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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201 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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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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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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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
282 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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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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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
52 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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1answer
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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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1answer
138 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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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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134 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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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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How To Calculate “İntermolecular Energy” as QM and MM? [closed]

In this article: http://ambermd.org/antechamber/gaff.pdf, in Table-7, authors have calculated "intermolecular energy" of a molecule set. I wonder how can I calculate this energy by using gaussian09 ...
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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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1answer
65 views

Computational Efficiency of Periodic Boundary Conditions

From what I understand, in a molecular dynamics simulation the number of molecules included is limited by the computational power available. In order to simulate macroscopic properties, one needs to ...
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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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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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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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163 views

Amber paramfit “monomer (or ligand)” problem [closed]

I am trying to parameterize a novel molecule which has atoms not included gaff or parm force field. I finished parameterizing vdw-bond and angle force field. Also I did PES Scan for dihedrals and I ...
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1answer
489 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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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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1answer
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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
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Constructing potential energy surface of a periodic system, how to deal with atoms moving out of the supercell?

I'm using NVE ensemble for doing molecular dynamics (MD) simulations. The periodic system I'm working with contains $50$ atoms and the "calculator" for calculating potential energies and forces is a ...
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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
224 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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1answer
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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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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 ...