Questions tagged [molecular-dynamics]

For questions related to the use of or theory behind classical or ab initio molecular dynamics.

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How would one find a material's equilibrium structure at any specific temperature?

Let's take an example of a simple FCC material, a binary alloy. Above absolute zero K, the alloy will start to disorder and become an FCC solid solution. The alloy would develop defects as it ...
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How do we study solid state reactions using atomic scale/electronic structure modelling?

How are different flavours of DFT or MD useful in the context of reaction mechanism modelling in solid state reactions like those that happen when green bodies (powders of metals along with C or N) ...
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How to reproduce 2D small-angle X-ray scattering (SAXS) interferogram of water via ab-initio MD methods?

I am trying to reproduce the 2D SAXS interference pattern of bulk water via ab initio MD methods as shown in the figure below: The main aim is to recreate figure (a) via averaging MD configurations ...
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187 views

Constraining coordination or bond lengths for certain atoms in VASP

I have a structure composed of many MX4 tetrahedral units. When doing MD on this structure I find that just one M atom moves into a trigonal planar coordination (MX3). I was wondering how to set ...
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How to make input script file for nanoparticle using LAMMPS?

Hope you're all doing well. I am a student of Doctorate in Beijing Institute of Technology. We are working on a project "DNA Regulated Nanozyme". and we intend to build an interaction ...
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114 views

Quantum chemistry in external electrostatic field?

Which quantum chemistry methods can be used in an external electrostatic field? Also which software supports that? I'm interested in anything from semiempirical (eg XTB) to DFT (eg ωB97, B3LYP-D3) ...
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Very slow performance for an OPLS-AA methanol simulation

I am running a methanol simulation with a topology I obtained from Tinker for OPLS-AA, at 298 K and 1 bar. This is my .itp file: ...
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1answer
70 views

How to fix "bad timestep" error in LAMMPS?

I'm working on this project where I have to simulate a gold nanoparticle impact in a gold plate, my script is: ...
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1answer
152 views

Calculating compressibility from a molecular dynamics simulation: what is meant by "volume fluctuation"?

I am trying to calculate isothermal compressibility from an NPT molecular dynamics simulation, but am not that experienced and don't know how to use an expression from a paper to do it. The part that ...
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1answer
59 views

Radial distribution function for trajectories or time frame?

In many scripts I came across, I saw for the calculation of the RDF, both the trajectory and the individual timeframe also have been used. Can anybody help me with understanding how they are different ...
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Apparent conservation of potential energy in NPT simulation?

I was examining a system with a problematic equilibration (more details given at the end, but probably unnecessary to answer the question), and came upon what is presumably a pretty basic conceptual ...
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57 views

Lone pairs in CHARMM for molecular dynamics [closed]

I have a substrate that has a Br-C bond. In CHARRM the line below is included in the .str file: ...
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4answers
577 views

How should one choose the time step in a molecular dynamics integration?

Choosing too small of a timestep leads to an unrealistic simulation time, whereas too big of a timestep leads to the system not being represented correctly (or, in the case of an algorithm like SHAKE, ...
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54 views

How do you Select a Time Step for Molecular Dynamics Simulations?

It seems there is a general agreement among the practitioners of Molecular Dynamics that 1fs is a fairly reasonable time step, with shorter time steps being required for materials with higher ...
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34 views

What's the pair correlation function? And what information we can read from it?

This question is related to this VASP tutorial, in which the pair correlation function (or radial distribution function: RDF) is utilized to justify whether the solid silicon is melt by AIMD (ab-...
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1answer
110 views

What does vacuum signify in the simulation box after the simulation?

While carrying out constant volume simulations, I've observed that sometimes when the gaseous molecules come closer from their initial spacing, an empty space is created in the box. As I should ...
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215 views

What is the real reason behind the minimization of the system at the beginning of a Car-Parrinello MD calculation?

I've been studying MD and more specifically about Car-Parrinello Molecular Dynamics and I'm not entirely sure if I understood the meaning behind the minimization. This is the way I understand it: The ...
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Chemical Structure of Iron Manganese Silicate Nanoparticle (IMSN) Nanozyme?

Hope you're doing well. Actually I am working on a project related to DNA regulated Nanozyme and I have a nanozyme of mesoporous silica "Iron Manganese Silicate nanoparticle (IMSN) nanozyme"....
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44 views

Back-mapping Martini 3 coarse-grain to all-atom representations

I have a $10\mu s$ trajectory with 10,000 frames that I would like to backmap to atomistic representations so that I can compare my ensemble to experimental measurements. I am using MartiniTools for ...
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How to calculate radial distribution functions for MD trajectories without PBC, directly from coordinates with python?

I have been running MD simulations on water droplets with an ion in them. I am trying to implement a python program that could calculate the radial distribution function from ion to oxygen (or ion to ...
5
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1answer
63 views

What is the equilibrium bond length for a Lennard-Jones potential?

If I have $\epsilon$ and $\sigma$ can I calculate equilibrium distance $r_e$ in one run? What I have tried is to put $V = \epsilon$ and bring out the $r$ from the formula, but it seems not solvable. ...
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1answer
89 views

How can one computationally determine the flammability of a molecular system?

I can imagine one aspect of flammability (the ability of a substance to ignite on fire) to include calculating the kinetics and thermodynamics of the reaction of the system with oxygen. This is not ...
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How to analyse structure factors calculated from a mixture of isotropic amorphous substrates

I am looking for a way to computationally analyse the interactions between two molecular species (as solute and solvent) in an isotropic mixture using X-ray scattering. Is there a guideline as to how ...
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1answer
61 views

How can I quantify the uncertainty of thermal molecule properties in molecular dynamics simulations?

When doing molecular dynamics simulations, there are countless sources of error (i.e. approximations and numerics). Molecular dynamics can be used to determine intrinsic thermal properties such as ...
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Setup for 4-point flexible water model

I tried to search online if there are examples or suggestions on how to setup a 4-point flexible water model, such as TIP4P/2005f, qTIP4P/f, TIP4P/$\epsilon$ FLEX, etc. but there's no clear example on ...
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How do I model drug diffusion from polymeric matrix?

I have been redirected to this forum from Chemistry SE. My problem consists of a structure (say a cylinder) made from a homogenous distribution of a drug from a polymeric matrix. These compounds are ...
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How to calculate small and wide-angle X-ray scattering spectra for the hydration shell restricted by a distance radius criteria

My main aim is to extract the SWAXS spectra for the hydration shell surrounding a solvated molecule and I am unfamiliar with the idea of excluded solvent volume. I tried looking online but many ...
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3answers
186 views

Limitations of pairwise additive forcefields

What are some of the limitations on the use of a pairwise additive forcefields in classical molecular dynamics simulations?
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1answer
56 views

LAMMPS input card in an NVIDIA GPU

I want to simulate the attached model for a Cu NP in Ar using my GPU, but I got erratic results. All looks well when I simulate it in my CPU with the command: ...
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1answer
61 views

List of software for creating random multi-component alloy inputs for DFT or MD

I'm looking for a list of tools similar to ATAT which are available for creating random multi-component alloy inputs for DFT/MD.
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2answers
818 views

Flying ice cube effect in molecular dynamics?

I am trying to understand what exactly the flying ice cube effect is, and how it manifests itself in MD simulation. From what I have read about it, I see that as we run certain forms of velocity-...
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1answer
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Where can I find/generate force-field parameters for common inorganic anions in water?

I have to do simulations of some inorganic anions, specifically $\ce{PO4^3-}$ (ortho-phosphate), $\ce{CO3^2-}$ (carbonate), $\ce{SO4^2-}$ (sulfate), in an aqueous enviornment. However, I am having a ...
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2answers
145 views

Methods to handle non-ergodic systems with Molecular Dynamics

Given the large difference between simulation timescales and the timescales on which we normally interact with ensembles of molecules, the time average of a molecular dynamics simulation does not ...
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Understanding the rigorous bridge between atomistic and coarse-grained simulations

I am currently reading this paper by Noid et. al. on the rigorous bridge between atomistic and coarse-grained simulations. In the paper, he defined a linear map from the atomistic coordinates and ...
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408 views

How can I modify the Martini v2 or v3 force field to increase the Lennard Jones potential well depth (epsilon)?

I am trying to run some coarse-grained simulations of an Intrinsically Disordered Protein (IDP) using the Martini force field, and I want to increase the strength of interaction between water and ...
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3answers
397 views

MD: How to estimate number of timesteps to converge a property

If I want to equilibrate a NPT system until a property reaches its equilibrium value (let’s say the volume V), what is the common practice to have a rough estimate of the total simulation time ...
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Is "Valence Electron Density" and "Electron Density" data of a molecule the same thing? [closed]

I'm wondering specifically in the context of calculating physical properties from valence-electron-density data using DFT, MD, and or ML (machine learning).
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1answer
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Should I use a different cut-off scheme for non-bonded interactions when simulating a system with MD in vacuum?

I am currently doing a simulation of the behaviour of various sizes of water droplets (~100-1000 water molecules) in vacuum. I am using NAMD with the spherical boundary conditions to keep the droplet ...
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Is it possible to experimentally verify this collision rate formula?

Background Let's say I have the $i$'th gas molecule with velocity $\vec v_i(t)$ at time $t$. To find the net displacement $s_i$ we integrate with respect to $t$: $$ \vec s_i = \int_{0}^{t} \vec v_i(t')...
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Where to get Tersoff and SW potentials for LAMMPS

I want to do some molecular dynamics simulations for silicene with hydrogen and halogen atoms deposited at the surface. Where can I find Stillinger-Weber potentials to use for this? There doesn't seem ...
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Molecular dynamics with surfaces

I want to run molecular dynamics with LAMMPS, the aim is to simulate a platinum surface with a gas phase consisting of simple molecules. I would like to use periodic boundary conditions in order to ...
6
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1answer
44 views

Can we assume that the intraceullular pH and intermembrane pH are the same when calculating the protonation state of a protein subunit?

I want to know the protonation state of the intermembrane subunit of a protein. For that, I need to know the pH, so given that small molecules can cross the lipid bilayer, could we assume ...
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1answer
134 views

How to address the errors on Automated Topology Builder?

I was trying to get the charges and the topology file for this molecule ($\ce{C28H58O7S8}$). But I get the following error despite using the right number of hydrogens. ...
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Molecular dynamics to reproduce dispersion interactions

I'm trying to simulate the behavior of chromophore molecules incorporated into a polymer under an external electric field. I've tried to use classical molecular dynamics (GROMACS) but it's unable to ...
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Practical way to reduce pressure fluctuations in molecular dynamics? [closed]

I am running a test setup in LAMMPS. I am using $4000$ atom hcp system with MEAM potential. The system need to be at equilibrium at $\pu{10K}$ and for this I am giving initial velocity at $\pu{10K}$ ...
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1answer
270 views

How should I generate a radial distribution function (RDF) for an MD trajectory with python?

I am attempting to analyse the radial distribution function (oxygen to oxygen) for a ~400ps simulation on a droplet of water (MD done with NAMD). I am using the python library MDAnalysis to do this. ...
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832 views

References for Molecular Dynamics?

I am new to the world of Molecular Dynamics (zero practical experience), and I know that a starting point to really go into the back-bone of MD is Statistical Mechanics (took a semester course in ...
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References for Electrostatics Calculations Used in Molecular Dynamics

I'm looking for classic references that describe the usual electrostatic contributions which have to be calculated in molecular dynamics simulations. I find it very hard to apprehend what different ...
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1answer
304 views

Error in GROMACS for adding ions to a solution

I am following Justin Lemkul's GROMACS simulation given on this website here for GROMACS. I believe I have followed the process to the T. I would like to mention that in the "Generate Topology&...
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2answers
298 views

What are good resources to learn Materials Modeling?

I wonder if there are any books or resources to start learning Materials modelling using methods density functional theory quantum monte carlo molecular dynamics