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Questions tagged [molecular-dynamics]

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

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3 votes
1 answer
50 views

How to calculate height of the center of the H2 molecule from surface via ASE?

I have XDATCAR file, i want to calculate graph of time vs height of the H2 molecule(center of the H2 molecule) from surface. ...
4 votes
0 answers
30 views

Relation between force constant of the bonded parameters, time constant and the dynamics of the system

I want to understand these things in both intuitive and non-intuitive ways. In some cases, we constrain hydrogens so that we can run molecular dynamics at a higher time step than we normally would, ...
3 votes
2 answers
64 views

Check for steric clashes before doing minimization

Are there already some tools available, or we can code for finding the atoms/residues that can contribute the steric clashes before minimization solve the issue?
2 votes
1 answer
24 views

LAMMPS structure rotation

I need to rotate half of the structure 180 degrees, I was able to do this operation but the rotation cannot be made symmetrical, do you have any ideas? commands I used: end result:
5 votes
1 answer
45 views

Forcefield parameterization techniques

Suppose I have a novel synthetic protein. I want to find the classical forcefields that accurately models the dynamics and thermodynamics of the protein. How do I do that?
2 votes
0 answers
42 views

Green Kubo Relation

I am calculating viscosity of WCA fluid using the Green Kubo relation. I am also following the paper of Zhang et al. for the Time decomposition method https://doi.org/10.1021/acs.jctc.5b00351 where, ...
1 vote
0 answers
26 views

How the center of mass of a large number of atoms influences the performance of Amber in a system?

I'm interested in conducting umbrella sampling between a ligand and the center of mass of a lipid. Initially, I chose the atom numbers for the ligand and all the atom numbers for the lipids. However, ...
5 votes
1 answer
69 views

Visualize variation of lattice parameters with temperature after MD

I am interested to plot lattice parameters vs temperature after Molecular Dynamics calculation in NPT ensemble to detect structural phase transition of my system, Ex- So, I am looking for python ...
6 votes
1 answer
111 views

Explain ab initio molecular dynamics like I'm five

In Kashiwaya, S., Shi, Y., Lu, J. et al. Synthesis of goldene comprising single-atom layer gold. Nat. Synth (2024) monolayers of hexagonal Au(111) planes are produced and released into solution where ...
22 votes
3 answers
2k views

What are the types of ab initio Molecular Dynamics?

I am new to the world of Molecular Dynamics, and am curious to know exactly what is considered to be an ab initio Molecular Dynamics (AIMD) method, and how do they work? The seminal work by Roberto ...
11 votes
1 answer
287 views

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 ...
4 votes
1 answer
101 views

Energies from single points vs. AIMD for training Machine Learning Force Fields

I am currently training a force field using machine learning techniques. One way to test the performance of the ML model is to use the force field for a production run (= molecular dynamics) and ...
7 votes
1 answer
55 views

Force fields for generating **Co3O4 and Fe3O4 structures in LAMMPS

I am working on a project that requires generating a large dataset of Co3O4 and Fe3O4 structures under various temperatures and pressures using LAMMPS. The structures will be used for training machine ...
7 votes
2 answers
650 views

Is it possible to build a force field that suits all elements based on VASP's machine learning result?

I have tried to use VASP's machine learning force field calculation during running molecular dynamics simulation with a supercell including some elements of Ti, O, Cu, etc. It does increase the speed ...
2 votes
0 answers
44 views

How to rotate a periodic structure in LAMMPS?

I want to rotate a periodic structure like this one by a 10 degrees around a z-axis (perpendicular to the plane) that goes through the center of the simulation box. After writing this in LAMMPS, <...
8 votes
5 answers
754 views

How to identify small molecules in a structure without bonds

If I have an XYZ file with a cluster of a dozen of molecules: water, $\ce{O2}$, $\ce{H2}$, $\ce{H2O2}$. A human may easily identify these molecules. But how to do it automatically? I need to identify ...
2 votes
1 answer
45 views

Problem with 'Thermo and fix ave not computed at compatible times' in LAMMPS

I followed the tutorial (https://github.com/lammps/lammps/blob/develop/examples/KAPPA/in.heat) to compute the thermal conductance of bilayer graphene sandwiched by Al2O3 on both sides along the z axis....
3 votes
0 answers
55 views

Hydrogen bonding rate of relaxation on molecular dynamics

I am studying the works of Alenka Luzar on the hydrogen bonding kinetics in liquid water. Luzar defines an autocorrelation function c(t) that gives the probability that an hydrogen bond is intact at ...
2 votes
0 answers
50 views

How to use interatomic potential in LAMMPS

This is my input file for the lammps simulation. ...
5 votes
0 answers
31 views

How can calculate length or coordinate of any molecule in different quantum state [like (rotational quantum state)j=2] with any software or code?

How can one determine the bond length of a diatomic or tri-atomic molecule(rot. state J=3 and vib. state v=2) from its ground state bond length (x angstrom) using computational tools or programming ...
5 votes
1 answer
47 views

Optimum number of CPUs to use for an efficient LAMMPS simulation

Are there any rules of thumb to optimize the number of CPUs to perform a LAMMPS simulation of a given size efficiently? For example, there are 32 cores under each node in my computational resource. ...
3 votes
0 answers
59 views

Lost atoms in a lammps simulation

I am simulating the thermal conductance along the z axis for bilayer graphene sandwiched by Al2O3 system. This is my input setting. ...
8 votes
3 answers
329 views

Hydrogen bonding autocorrelations

I am currently analyzing hydrogen bonding behaviour and kinetics with molecular dynamics simulations. I've been trying to compute autocorrelation functions for hydrogen bonds in a water system. Some ...
7 votes
2 answers
201 views

How to add atom attribute molecule for each layer in LAMMPS?

I want to model several layers of hBN in LAMMPS. First, for two layers, I created a lammps data file from vasp POSCAR using atomsk. It is like this: ...
7 votes
2 answers
369 views

Restrain a protein to be helical in an MD simulation

I have a very small part of a protein that is supposed to be helical. However, in molecular dynamics simulation, it unfolds and gets into extended conformation. Is there any way I can force it to stay ...
3 votes
0 answers
22 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 ...
3 votes
0 answers
32 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 ...
6 votes
2 answers
230 views

Are there scripts available for AIMD?

I need to determine which of two electrolyte is the best for a hydrogen fuel cell. As far as I understand, the first thing to do is to compute their ionic diffusion coefficient and to compare (the ...
4 votes
0 answers
73 views

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 ...
4 votes
0 answers
42 views

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 ...
4 votes
1 answer
82 views

Thermal vs dynamical stability

Dynamical stability is checked by a phonon curve. Thermal stability is checked by a molecular dynamics simulation. What is the difference between them?
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 ...
3 votes
1 answer
133 views

How to convert a SMILES into a LAMMPS or GROMACS input file?

Are there any dedicated Python tools/packages/scripts that help me convert a SMILES structure into an MD coordinate and topology file (both for GROMACS and just the single one for LAMMPS)? Demonstrate ...
6 votes
2 answers
371 views

Calculation of pH in Molecular Dynamics simulation?

I have a system that has 5M aluminum hydroxide (10 molecules) ion [Al(OH)4]- and 5M NaOH (10 molecules) in a box of side length 15 angstroms each. I have 113 water molecules in the system, so that the ...
4 votes
2 answers
91 views

Given a .gro file of a monomer, how to polymerize it?

I have a structure (.gro) file of a PolyEthylene Glycol (PEG) molecule as shown below. How do I get the corresponding structure file for PEG-20 i.e., a molecule with a degree of polymerization=20, ...
5 votes
1 answer
77 views

How can one create various arrangements of two or more types of atoms (like O, N etc.) with distinct coverages on a metal surface?

How can I modify the procedure described in this answer to achieve adsorption of two or more types of atoms on a surface, each with distinct coverages? Is there an extension to the described method ...
7 votes
0 answers
30 views

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 ...
5 votes
1 answer
67 views

How can I specify the direction of motion in the colvars file?

I am doing umbrella sampling in NAMD and I want to control the distance in the colvars to be in one direction. Is there any possibility?
2 votes
1 answer
30 views

How can a harmonic constraint be added between two groups in one direction using NAMD?

As a new user of NAMD, I am seeking assistance regarding a specific task. I intend to pull a LIGAND from outside to the center of a lipid using NAMD. To achieve this, I have utilized the colvar module ...
4 votes
0 answers
39 views

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 ...
4 votes
0 answers
72 views

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 ...
2 votes
1 answer
58 views

How to write the REBO force field

I want to use the REBO-CHO force field to study graphene oxide using lammps. But I don't know how to create the input file with the parameters by reading the article or if there is a tutorial or ...
4 votes
1 answer
100 views

Advantages/Disadvantages of Qeq over Drude polarizable model?

For classical Molecular Dynamics (cMD) simulations, the usual methodology is to use force fields (FFs) with fixed point charges (examples include CHARMM, AMBER and Gromos). However, this approach ...
3 votes
2 answers
62 views

My CHARMM IC table generation has caused hydrogen to bond to two carbons. How do I fix this?

As above, I am attempting to generate an IC table for decanoic acid using CHARMM (version 48b1) so I have a minimized geometry. I have attached my build.inp script and the stream file I have written. ...
3 votes
1 answer
131 views

Controlling Initial Velocities in NVE Trajectory Simulations with VASP

"I've determined the initial velocities of the surface following its equilibration at 300 K in the NVT ensemble. Now, I aim to conduct AIMD (NVE ensemble)with the metal surface (initially defined ...
1 vote
1 answer
89 views

How to compute the Elastic Modulus of a molecule using GROMACS?

Say we take the basic example of a PEG molecule (PolyEthylene Glycol). What is the fundamental physics for computing the Elastic Modulus or the Young's Modulus from the Molecular Dynamics (MD) ...
2 votes
1 answer
127 views

Velocity autocorrelation function for molecular dynamics trajectory

I have a 1 ns long molecular dynamics trajectory of 884 molecules of water, and I am trying to compute the velocity autocorrelation function using MDAnalysis to analyze the GROMACS output files. I ...
2 votes
0 answers
94 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 ...
1 vote
1 answer
78 views

What is the best way to optimize molecules with 8000 atoms. This includes C,H,O,N,Si

My molecule includes C,H,O,N,Si
2 votes
1 answer
21 views

Geometry of H2O in the v=1 vibrational state for AIMD simulation

This is a follow-up to my recent question: Algorithm for finding the v=1 state of an H2O molecule I want the geometry (atomic positions) of the H2O molecule in the v=1 state. How are initial ...

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