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 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: ...
Vladislav Gladkikh's user avatar
8 votes
2 answers
278 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 ...
horlust's user avatar
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6 votes
4 answers
704 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 ...
user36313's user avatar
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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
  • 459
6 votes
3 answers
354 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 ...
Roshan Shrestha's user avatar
4 votes
0 answers
63 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 ...
Hemanth Haridas's user avatar
6 votes
2 answers
221 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 ...
Mjf T's user avatar
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4 votes
0 answers
41 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 ...
AlfredV's user avatar
  • 183
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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4 votes
1 answer
79 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?
ArduinoEnthusiast's user avatar
6 votes
2 answers
351 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 ...
Hemanth Haridas's user avatar
7 votes
0 answers
27 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 ...
Mike's user avatar
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5 votes
1 answer
63 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?
Abd-Elazeem Mohamed's user avatar
2 votes
1 answer
28 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 ...
Abd-Elazeem Mohamed's user avatar
5 votes
1 answer
71 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 ...
Rubi Agrawal's user avatar
4 votes
0 answers
36 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 ...
Hemanth Haridas's user avatar
2 votes
1 answer
52 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 ...
Matías Eduardo González Ozuna's user avatar
4 votes
1 answer
98 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 ...
Hemanth Haridas's user avatar
4 votes
2 answers
87 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, ...
Pranoy Ray's user avatar
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4 votes
0 answers
71 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 ...
bhopshang's user avatar
  • 233
3 votes
1 answer
90 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 ...
Rubi Agrawal's user avatar
2 votes
1 answer
86 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 ...
horlust's user avatar
  • 133
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
  • 141
1 vote
1 answer
66 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) ...
Pranoy Ray's user avatar
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2 votes
2 answers
57 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. ...
Thomas's user avatar
  • 81
1 vote
1 answer
75 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
AKM's user avatar
  • 11
2 votes
1 answer
20 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 ...
Nidhi Tiwari's user avatar
2 votes
0 answers
39 views

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
1 answer
61 views

Equilibrating Surface Temperature Through NVT Ensemble Ab Initio Molecular Dynamics

In my AIMD simulations with the NVT ensemble at T= 300K (Nosé–Hoover thermostat)for a Pd (111) surface (2*2, 6 layers) and vacuum sizes of 14 Å and 18 Å, All other INCAR tags are same(only NGZ for 14Å ...
Rubi Agrawal's user avatar
2 votes
0 answers
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
6 votes
1 answer
180 views

Speed of atom from kinetic energy of molecule

What is the velocity of each hydrogen atom in an H2 molecule, given a kinetic energy of hydrogen molecule is 0.12 eV, when expressed in angstroms per femtosecond and assuming equal velocities for both ...
Rubi Agrawal's user avatar
1 vote
1 answer
76 views

How to use martinize.py?

I have been trying to get the CG representation of a basic octane molecule. The pdb file is as follows: ...
Pranoy Ray's user avatar
  • 1,631
3 votes
1 answer
110 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 ...
Pranoy Ray's user avatar
  • 1,631
4 votes
1 answer
40 views

phase average uncertainty in molecular dynamics

I was wondering if I could find some scaling relation of the uncertainity of phase averages of thermodynamic quantities with the number of atoms $N_a$, the number of timesteps $N_t$ and size of the ...
n1ps's user avatar
  • 41
3 votes
0 answers
35 views

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
2 votes
1 answer
173 views

Choice of SMASS for AIMD simulations in VASP

How can one verify that the values (0, 1, 2, and 3) in the SMASS parameter correspond appropriately to the NVT ensemble(Nose-Hoover thermostat) in the context of an ab initio molecular dynamics ...
Rubi Agrawal's user avatar
3 votes
1 answer
140 views

having trouble to get the NPT working

I am currently encountering challenges in successfully conducting NPT simulations in LAMMPS for a triclinic cell persistently remain unchanged throughout the NPT simulation.my input file is: ...
Ati's user avatar
  • 31
6 votes
0 answers
107 views

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
  • 121
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
  • 21
2 votes
1 answer
46 views

How to make initial trajectory for incident A2 molecule on any surface?

I want to write code to simulate the impingement of any molecule on a surface at different (r, theta, and phi) angles in XYZ format.
Rubi Agrawal's user avatar
4 votes
0 answers
100 views

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
6 votes
0 answers
122 views

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
  • 121
4 votes
1 answer
36 views

Is water penetration and fatty acid dissolution reasonable when Gromacs modelling of an aqueous lipid bilayer?

as mentioned, I'm building a molecular dynamics simulation of decanoic acid and decanoate (with neutralising sodium cations) in water. I've minimized and equilibrated the simulation up to 295 K and I'...
Thomas's user avatar
  • 81
4 votes
0 answers
177 views

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
  • 41
4 votes
1 answer
124 views

How do we calculate diffusion coefficient when GROMACS MSD graph with two slopes?

I calculated the MSD using the gmx msd -f run05.part0005.xtc -s run05.tpr -o msd_200-250ns.xvg. As a result, I got a graph with 2 slopes as attached. In the MD simulation, I followed a simulated ...
Ema 's user avatar
  • 43
6 votes
1 answer
100 views

Lattice constant of an FCC crystal from molecular dynamics simulation

So, I have a system of n number of molecules inside a box which is supposed to be solid. I performed the md simulation of the system using stochastic integrator in a box. I know the lattice of the ...
Roshan Shrestha's user avatar
4 votes
1 answer
65 views

DFPT vs analytical nuclear gradient

I have read some literatures about the gradient wrt. atom positions of the DFT energy, and find different methods one commonly used in MD(analytical nuclear gradient,pulay's paper), and another ...
Fadelis Hu's user avatar
4 votes
1 answer
206 views

Random velocity generation

How to generate random velocities in the geometry coordinates of a surface (POSCAR file) using the Boltzmann distribution law with Atomic Simulation Environment (ASE) or other codes for Molecular ...
Rubi Agrawal's user avatar
1 vote
0 answers
36 views

LBFGS -- Incomplete Convergence due to BadIntpln [closed]

I am doing energy minimization of a molecular system in TINKER. While doing so, I am getting the error in the title of this question. What might be my problem?
Himanshu's user avatar

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