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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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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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
42 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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How to compute for the ATP molecule that can be produced from 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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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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1answer
130 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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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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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
247 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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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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How to use potential energy surface represented by a neural network for molecular dynamics simulation?

I trained a neural network that represents the potential energy surface of a periodic system consists of $50$ atoms. The neural network takes the structure proposed by Behler and Parrinello in 2007. ...
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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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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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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 ...
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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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1answer
97 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) ...
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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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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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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 ...
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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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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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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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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: ...
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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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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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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 ...
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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 ...
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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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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 ...
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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 ...
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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 ...
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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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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}{...
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How can you simulate the effect of a solvent on a polymer in an MD simulation?

I'm doing a molecular dynamics simulation of polymer melts and I want to include the effect of a good/bad solvent on the melt. How can this be done? My simulation models polymers using a bead-spring ...
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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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What is the “curse of dimensionality” in molecular dynamics?

The 'curse of dimensionality' or the 'bottleneck problem' in molecular dynamics is explained in page 5 and 6 of Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods by Dominic Marx and Jurg ...
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How to perform molecular dynamics simulations of charged systems?

The GROMACS official documentation (see here) states that a system with non-zero total charge will yield an error: System has non-zero total charge Notifies you that counter-ions may be ...