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 to go from zero to hero in Machine Learning for materials modelling

I am interested in exploring the use of machine learning tools to accelerate molecular dynamics simulation probably by training machine learning potentials. While I have found some papers that apply ...
manuelpb's user avatar
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DIY molecular dynamics for Xenes on crystal surfaces; where can I get applicable open-source force field parameters that I can use in my scripts?

The linked question(s) below describes a DIY project to simulate how Xenes (honeycomb nets of atoms like graphehe) behave on single crystal surfaces. Behaviors include rotation, strain, and heigh ...
uhoh's user avatar
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Contribution in action from collisions for a gas?

So if I write the action for a gas: $$ S = \int (T -U) dt \tag{1}$$ where $T$ is the kinetic energy and $U$ is potential energy. I suspect there is a constant term (which does not affect the equations ...
More Anonymous's user avatar
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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 ...
mykd's user avatar
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Question about Constructing Supercell Layers for MD Simulations for Solid-Solid Phase Transitions

I am a newcomer to MD simulations, so my questions may be at a basic level, but I appreciate your understanding. I would like to simulate solid-solid phase transitions using MD simulations. To begin ...
Mike's user avatar
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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 ...
mykd's user avatar
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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 ...
mykd's user avatar
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Why is potential energy used and not total energy when calculating free energy?

I have run a replica-exchange molecular dynamics simulation, using a number, $n$, of replicas initiated at the same number, $n$, of unique temperatures. I have calculated the free energy profile over ...
napadia's user avatar
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Free energy calculation as a function of temperature over phase transition

I've run a molecular dynamics simulation (NVT) of a simple Lennard-Jones system of a few particles and I'm trying to calculate the Helmholtz free energy $\Delta F$ as a function of temperature over ...
napadia's user avatar
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Regarding use of GCMC to add water molecules

I am working on a goethite system, and wish to fill the unit cell with water molecules for AIMD simulation using quantum espresso. For this, some papers[1],[2] indicated the use of Grand Canonical ...
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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 ...
Barbaud Julien's user avatar
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2D Infrared spectroscopy for bulk systems using molecular dynamics

There are some questions and answers (1,2) on this site regarding simple infrared and vibrational density of states calculations with molecular dynamics and there any simple algorithmic descriptions ...
mykd's user avatar
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Loading Gromacs Trajectories using ASE (Atomic-Silumation-Environment)

I am trying to study some trajectories generated using Gromacs. I have been given tpr and pdb files of the simulation. What might be the most effective way to load them in ASE? Or is there way to ...
Saha_1994's user avatar
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Significant differences between NPT and NVT equilibrated simulations

I am performing a set of classical MD simulations using a type of ReaxFF description to study aluminate Oligomerization. I have performed two sets of simulations, one where the system is equilibrated ...
Hemanth Haridas's user avatar
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MD simulations of liquid isopropanol predicts wrong thermodynamics proprieties

I am using GROMACS to run molecular dynamics simulations of pure liquids, in the NpT ensemble at room temperature and p = 1 atm. My first test was with isopropanol (also known as 2-propanol). I used ...
AlfredV's user avatar
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Modelling excited states using classical MD simulations

My question is related to the question here but not exactly the same. The studies which have looked into the excited states of molecules have generally done it by parameterizing the ground-state and ...
Hemanth Haridas's user avatar
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Solvation_analysis subpackage for MDAnalysis multi-atom solute

I have a simulation trajectory from DFTB+ for 1 NaNO3 in 32 H2O molecules. The trajectory is in xyz format and I converted a frame of xyz to pdb using openbabel to serve as topology input. I am ...
bhopshang's user avatar
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How to perform a rotation of a structure, specifically throughout molecular dynamics or umbrella sampling simulations?

I have a structure, as depicted in the figure, which is a part of a longer chain. The portion within the red circle is predominantly parallel. My objective is to rotate this part, aiming to orient the ...
Abd-Elazeem Mohamed's user avatar
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Free energy as a function of temperature over phase transition in molecular dynamics simulation

I've constructed a low density standard MD simulation (in Python), using the Lennard-Jones potential with an Andersen thermostat, of 10 particles in a box V = 10 $\times$ 10 $ \times$ 10 in the NVT ...
erkoo's user avatar
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How to extract Lindemann Index from LAMMPS dump files?

I used a python code to extract Lindemann index from dump files. But the problem is the code works fine with dump files with little amount of data and atoms. When I use large files if shows overflow ...
Lammps_beginner's user avatar
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ASE/XTB: zero temperature and stress in MD simulation

I want to see how the volume and pressure of my cell is changing during a MD relaxation in ASE. I used the atom.get_volume() and ...
Marco Di Gennaro's user avatar
4 votes
0 answers
53 views

OOM Error Calculating ESP Charges with Psi4

I'm trying to create a script to generate partial charges for a given .dat file. As an example of my process, I'm currently using gromacs to run minimization on a box of propane. It outputs a min.gro ...
asquith's user avatar
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MMGBSA: Electrostatic and van der Waals

I ran a molecular dynamics simulation using Gromacs 2023.2, with the CHARMM36 forcefield. And I ran a per-residue energy decomposition calculation using gmx_MMPBSA, with MMGBSA model. MMGBSA model ...
Bruce Zhou's user avatar
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Quantifying binding free energy?

I have binding free energy of some organic molecules on a surface, computed through Umbrella sampling. For now, I only have experimental data on the binding energy of some of these molecules. Is it ...
Roshan Shrestha's user avatar
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How to create a water droplet (half-sphere) on a rock (quartz) surface

I am to Equilibrate a uniformly distributed spc water molecules at 300k in 50x50x50 box. Water density is taken to be 1000kg/m3. Simulate the system in the NVT ensemble. The spc water is modeled using ...
Abdul Rauf Kaunda's user avatar
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Density of a spherical droplet of water on top of graphene

I produced a spherical droplet of water by having a box of water (sufficient water molecules inside the box to give the right density of water) on top of a 2d sheet-like graphene. The box becomes a ...
Roshan Shrestha's user avatar
3 votes
0 answers
18 views

Can ACEMD be implemented with OpenPathSampling

Is it possible to implement ACEMD with OPS? I am asking in the context of using NNP/MM models with OPS. The paper "NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning ...
Varun Gopal's user avatar
3 votes
0 answers
25 views

How to set up the NEMD (Non-Equilibrium Molecular Dynamics) calculation in LAMMPS

Suppose a benzene ring is connected with copper nanorod on both side along the z axis and they compose the scattering region. On both sides of the scattering region along the z axis, the left and ...
Kieran's user avatar
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3 votes
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Compute the monomeric fraction in MD simulation

I have a system of molecules in two different solvents in which aggregation occurs, but visually in different ways. In one, aggregation occurs rapidly, but in another sparsely. These MD simulations ...
Roshan Shrestha's user avatar
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34 views

How to perform atomistic spin dynamics (ASD) Ab Initio Molecular Dynamics (AIMD) using VASP?

I have tried normal AIMD simulation using VASP for Non magnetic materials. Now, I am interested to perform the molecular dynamics simulations for the finite temperature for Magnetic materials to ...
prakash g's user avatar
3 votes
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How to get energy gap change at specific high symmetry points during ab initio molecular simulations?

I want to check the energy gap change during finite temperature ab initio molecular simulations. The results may look like this picture: How can set aimd simulation to get this result in VASP?
Tieyuan Bian's user avatar
3 votes
0 answers
138 views

Read and run lammps water model in ASE

I want to read a lammps data file in ASE, for instance the TIP3P or the SPC model. The lammps examples provide the input script and the data file, which work perfectly. ASE is not able to read the <...
Marco Di Gennaro's user avatar
3 votes
0 answers
46 views

Running molecular docking simulation between two proteins

i did run docking simulation between two proteins on HADDOCK server but now i want to run a simulation of complex (protein+ligand and protein) is it possible with HADDOCK and how can i use it best ...
Imane Yamari's user avatar
3 votes
0 answers
180 views

How to check the units from ASE get_forces() function?

Here is a little python code that loops through a molecular dynamics trajectory (performed with the ASE package) and outputs the forces on the atoms at each frame: ...
breadcrumbs's user avatar
3 votes
0 answers
47 views

Is it possible to find a cubic supercell for a non-cubic crystal structure?

Suppose that we have a crystal material with a non-cubic unit cell. E.g. $\alpha \neq \beta \neq \gamma \neq 90^{\circ}$. Is it possible to find a supercell such that $\alpha = \beta = \gamma = 90^{\...
ado sar's user avatar
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Are the Lagrange multipliers used in Kohn-Sham DFT/HF-based quantum molecular dynamics real valued?

I have seen it written in several places that the matrix of Lagrange multipliers used to impose orthonormality in quantum molecular dynamics schemes based on Kohn-Sham DFT or Hartree-Fock for instance,...
aQuarkyName's user avatar
3 votes
0 answers
50 views

Appropriate choice of force constant of spring to use for Steered molecular dynamics

As per Boltzmann distribution, the variance, or the fluctuation in length squared is given by $$\sigma^2 = \frac{k_BT}{k_{spring}}$$ Since $k_{spring}$ determines how strong the force I am applying to ...
Roshan Shrestha's user avatar
2 votes
0 answers
54 views

Prerelaxation before AIMD with VASP

I am investigating a bulk structure by ab initio molecular dynamics (AIMD) implemented in VASP. I was wondering, how to choose the initial geometry (= POSCAR file) to run the AIMD simulation. In the ...
Lukas's user avatar
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2 votes
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Error with running GROMACS with SLURM

I am running into errors while submitting a job for a basic MD Simulation with HPC on SLURM. My sbatch script reads as follows: ...
Pranoy Ray's user avatar
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2 votes
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24 views

Eliminate the entropic contribution in the free energy of dimerization between two molecules in umbrella sampling

For my set-up to compute the free energy of dimerization between two molecules in a solvent using umbrella sampling, I can see that there is an entropic contribution since I have used distance as a ...
Roshan Shrestha's user avatar
2 votes
0 answers
33 views

Help with understanding the method of MBD & MBD-NL

I am having a hard time understanding the steps of Tkatchenko's method of many-body dispersion (MBD) and nonlocal many-body dispersion (MBD-NL). I would greatly appreciate a detailed & clear ...
Reut S's user avatar
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Method for Energy Computation of Protein Structures

So far i have found only one paper that describes how we can compute protein energy while doing MD simulation: Nishikawa, Ken, Motohisa Oobatake, and Tatsuo Ooi. "Method for Energy Computation ...
user366312's user avatar
  • 2,506
2 votes
0 answers
151 views

Help with LAMMPS create_atoms and delete_atoms command

I am running polymer simulations inside a spherical region. I have loaded the polymer using read_data command. I want to add fixed number of individual new atom types inside this sphere while it ...
Roni Saiba's user avatar
2 votes
0 answers
46 views

Where should we compute `Trajectory` in this listing?

Cross-posted here. I have the following listing for a barebone MD simulation: ...
user366312's user avatar
  • 2,506
2 votes
0 answers
32 views

How to estimate the minimal distance between atoms for which a pseudopotential-based AIMD gets forces correctly?

I am doing ab initio molecular dynamics in VASP. As far as I know, pseudopotentials approximate all-electron potential far from the nucleus, and deviate from it near the nucleus. When some of my atoms ...
Vladislav Gladkikh's user avatar
2 votes
0 answers
32 views

Interaction energy of two cartesian quadrupoles?

I am looking for a complete description of the interaction of two traceless cartesian quadrupoles. Even just an implementation online would be quite useful. The problem I am having is many of the ...
jheindel's user avatar
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2 votes
0 answers
60 views

Simulate liquid solvent mobility through a gel polymer electrolyte

I would like to simulate a liquid solvent (such as TEGDME) embedded into a polymeric cage (such as PEGDM). What is the most meaningful approach to estimate transport properties in such a system? Three ...
Marco Di Gennaro's user avatar
2 votes
0 answers
35 views

How to bond two laminates (same material) separated by distance using compressive pressure in LAMMPS?

I would like to simulate the bonding process using compressive pressure for two layers of the same material. Applying a uniaxial strain and using the deform tag in LAMMPS requires PBC in all ...
user6363's user avatar
2 votes
0 answers
37 views

Literature applying molecular docking into MD-simulated structures of proteins

This is quite surprising, at least for me, that many papers performed molecular docking of an unsimulated (original) protein structure and MD simulation of a protein in a timescale to check the ...
làntèrn's user avatar
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1 vote
0 answers
18 views

Thermal Conductance along the lateral and longitudinal direction

Suppose the left and right leads are both copper rod and the central scattering region is one monolayer graphene sheet. There is no chemical bonding formed between Cu and C atoms. The copper and ...
Kieran's user avatar
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