Questions tagged [molecular-dynamics]

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

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5
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36 views

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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3answers
73 views

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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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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1answer
149 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 ...
6
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1answer
68 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: ...
6
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1answer
58 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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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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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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214 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 ...
5
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1answer
53 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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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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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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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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40 views

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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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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85 views

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 ...
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3answers
185 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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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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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.
6
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1answer
53 views

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
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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2answers
407 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 ...
10
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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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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 ...
8
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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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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 ...
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1answer
89 views

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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108 views

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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1answer
91 views

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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42 views

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 ...
10
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1answer
263 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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85 views

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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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 ...
6
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1answer
65 views

Secondary structure information at each frame in a VMD trajectory

I am trying to write a tcl script to measure percentage helicity at each frame of a VMD .dcd trajectory. I found the following discussion on the VMD mailing list to calculate the secondary structure ...
8
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1answer
317 views

I generated Wannier centers but am having trouble understanding how they relate to the atoms in my system: there are more Wannier centers than atoms?

I'm trying to calculate dipole moments from Wannier centers for the first time and there are basics I don't understand and can't figure out from online resources. The software I'm using has a simple &...
12
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1answer
152 views

Creating Interatomic Potential for Lammps using DFT

What are the basic steps and methodologies used in creating inter-atomic potential (specially EAM, MEAM potentials) for metals ...
7
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1answer
107 views

How do I build and run a simulation of water molecules in NAMD?

So, I have started to learn NAMD because I need that for a project I will be doing in the next couple of months. I have some prior experience of MD with gromacs. I thought that since NAMD has a GUI ...
4
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1answer
76 views

Simulating polymers using cellular automata?

I am a physics student, and I am working on my final year project, I am planning to simulate polymers using cellular automata. I am really struggling with this project, if someone can give me any ...
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0answers
83 views

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).
8
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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. ...
12
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1answer
62 views

What does this temperature & total free energy profile mean (obtained from VASP NVT molecular dynamics simulations)?

In order to obtain molecular dynamics (MD) simulations trajectory for computing phonon dispersion relation at finite temperature, I performed NVT MD simulation using VASP for my target system. Here is ...
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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6answers
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How do I simulate the interaction between two atoms?

I want to build a rough atom interaction simulator, where pushes two (or more) atoms toward each other and they should behave physically correctly: attract, bond or repel with some force. So that is ...
7
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1answer
55 views

How to calculate the volumetric energy density of a molecule?

I am trying to store hydrogen in a hydrocarbon. The example can be taken as cyclohexane ($\ce{C6H12}$) which is in a hydrogen-rich state. Its hydrogen-lean state is Benzene. I want to calculate the ...
7
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1answer
58 views

How to discard molecules at the boundary in the Atomic Simulation Environment (ASE)?

When building a supercell for a molecular crystal with the Atomic Simulation Environment, it seems that the program takes into account periodic boundary conditions when replicating the unit cell. How ...
3
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1answer
38 views

Missing residues in ATB downloaded pdb/rtp files

I have downloaded the diglyme molecule from the ATB server (http://atb.uq.edu.au/molecule.py?molid=34570#panel-md) Two files are available: a PDB file and a topology ITP/RTP file. The name of the ...
11
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2answers
62 views

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 ...
8
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2answers
215 views

Large pressure fluctuations in molecular dynamics

I'm performing MD simulations, using NPT ensemble. The problem is that the pressure fluctuates severely and doesn't average at required level. For example, I set the pressure at 1 bar and it averages ...
13
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1answer
150 views

Minimum image convention for non-orthorhombic unit cells

I am trying to take into account periodic boundary conditions for non-orthorhombic unit cells. I have the atomic coordinates for a monoclinic super cell with the following lattice vectors output by ...