Questions tagged [molecular-dynamics]

Molecular dynamics is a method in computational chemistry that is used to study the movement of atoms and molecules.

Filter by
Sorted by
Tagged with
3
votes
0answers
33 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 $\pu{0.36 nm}$ ...
2
votes
0answers
19 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,...
4
votes
1answer
69 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
votes
1answer
132 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 ...
3
votes
1answer
36 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. ...
7
votes
1answer
157 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, ...
3
votes
0answers
74 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 ...
-1
votes
1answer
138 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? ...
2
votes
0answers
44 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 ...
-1
votes
1answer
72 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 ...
1
vote
1answer
46 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. ...
0
votes
1answer
32 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 ...
1
vote
1answer
105 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 ...
7
votes
0answers
317 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 ...
3
votes
1answer
131 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 ...
4
votes
1answer
92 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 ...
1
vote
0answers
54 views

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 ...
2
votes
0answers
49 views

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 ...
1
vote
1answer
56 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 ...
1
vote
0answers
36 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.
6
votes
0answers
94 views

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 ...
2
votes
0answers
166 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 ...
2
votes
0answers
135 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 ...
2
votes
1answer
340 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 ...
8
votes
1answer
101 views

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 ...
1
vote
1answer
41 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 ...
1
vote
1answer
60 views

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 ...
2
votes
2answers
598 views

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 ...
2
votes
1answer
189 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 ...
4
votes
1answer
56 views

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 ...
2
votes
1answer
68 views

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 ...
0
votes
0answers
52 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-\...
2
votes
1answer
115 views

Calculate force on atoms given the energy of configuration, trajectory of simulation and position of atoms in each frame

Background I am using a neural network to calculate the potential energy of atoms in a configuration and then adding energy of all atoms to compare it with the true energy of the configuration(label) ...
1
vote
0answers
101 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 ...
8
votes
2answers
229 views

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 ...
1
vote
1answer
115 views

Calculating the x, y and z distances between two molecules - AMBER (Molecular Dynamics)

I am interested in calculating the x,y and z distance between two molecules over a given simulation time. I know how to calculate the total (r) distance between them, but I want the distance between ...
2
votes
0answers
207 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 ...
-1
votes
1answer
99 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 ...
2
votes
0answers
192 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 ...
1
vote
1answer
39 views

Separating two sugars according to their heavy atoms - Steered Molecular Dynamics

I am trying to separate two methyl-N,N'-diacetylchitobiose sugars using steered molecular dynamics in AMBER. I have tested out: ...
4
votes
0answers
141 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 ...
0
votes
0answers
51 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 ...
6
votes
2answers
438 views

Force Constants for Angles From Gaussian To AMBER: which value should I put in the matrix equation?

I am trying to make a new force field in AMBER for a novel compound including boron (which does not exist in GAFF). For this, I calculated freq and I found bond force constants but I couldn't find ...
8
votes
1answer
563 views

How to simulate phase separation in a discrete system using LAMMPS?

I would like to simulate phase separation in LAMMPS and need advice what kind of two particle systems and interactions will yield phase separation. For example, a meta stable phase separation is ...
1
vote
0answers
57 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 ...
14
votes
4answers
880 views

Why are MD (Molecular Dynamics) simulations performed at room temperature for the purposes of studying proteins?

All of the MD simulations which are cited in the literature seem to be performed at room temperature (~300 Kelvins), while enzymes are usually bioactive at body temperature (~310 Kelvins). I am ...
6
votes
1answer
262 views

How to write an entire trajectory into a single PDB file?

I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library. With VMD if I do ...
6
votes
1answer
75 views

What types of energies can be determined by molecular dynamics in gas phase or explicit solvents?

For molecular dynamics in the gas phase I've seen that electronic energy can be determined and also decomposed in kinetic and potential energy. I've also seen that we can include ZPE. But can we ...
3
votes
0answers
146 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 ...
10
votes
2answers
1k views

Boltzmann Distribution in Molecular Dynamics Simulation?

The Boltzmann distribution is often used to describe the population of energy states at different temperatures, i.e. something like $$\dfrac{g_i}{g_j} = \mathrm{exp}\left(-(E_i-E_j)\times \frac{1}{...