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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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How to decouple the Lennard-Jones (LJ) interaction between two particular atoms in a same molecule?

I would like to decouple the lennard-jones (LJ) interaction between two atoms of the same molecule. These atoms obviously doesn't have any bonded interactions between them, so only the non-bonded ...
Roshan Shrestha's user avatar
3 votes
0 answers
26 views

martinize issue

PS C:\Users\MALINE\Desktop\martini> python martinize.py -f polypropylene.pdb -o output.pdb ...
068 MALINE M's user avatar
3 votes
0 answers
29 views

LAMMPS: Start NVE simulation with different initial energies

I am new to LAMMPS and am using it to conduct microcanonical (NVE) MD simulations. I am able to run NVE simulations using the fix NVE command, but I want to start a series of simulations in parallel ...
KugelBlitz's user avatar
3 votes
1 answer
45 views

Creating train.cfg in mlip-2

I am trying to train a moment tensor potential (MTPs). For that I need to convert OUTCAR (from AIMD simulation) to train.cfg file as per instructions given in this (https://www.rsc.org/suppdata/d0/mh/...
Kratos1611's user avatar
2 votes
0 answers
21 views

How to Implement a Custom Calculator in ASE for a System with Two Particle Types?

I'm new to ASE and currently working on a simulation involving two types of particles, A and B, with quantities NA and NB respectively, within a simulation box of dimensions (4,4,4) in x, y, and z ...
Rivnat Chowdhury's user avatar
2 votes
0 answers
27 views

How to calculate the pressure of the system with molecular dynamics simulation

Suppose there are two different types of gas molecules, filling up a sealed container. Then, relax the gas system in this sealed container under -30 degree centigrade. After the full relaxation, how ...
Kieran's user avatar
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3 votes
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How do I fill my simulation box with molecules efficiently?

I am using VASP for DFT simulations so far and want to start with AIMD of solid liquid interfaces. Now I stand before the problem of how to fill my cell appropriately with molecules. So far I have ...
And's user avatar
  • 433
1 vote
0 answers
19 views

Fix the distance restraint between two set of molecules in gromacs

it seems that in GROMACS we can apply distance restraint between two atoms/particles. However, does anyone know if one can apply a distance restraint between whole two set of molecules, like apply a ...
Roshan Shrestha's user avatar
1 vote
0 answers
43 views

AMBER fails to generate parameters

I'm new to computational chemistry, and I'm trying to model the enzyme EGFR and a molecule named lapatinib with AMBER. I got a .pdb file of Lapatinib attached to EGFR, and a .sdf file of lapatinib ...
Leo's user avatar
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3 votes
0 answers
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Adding a molecule in AMBER

I'm new to computational chemistry. I want to model the enzyme EGFR and a small molecule Lapatinib. I got a .pdb file of EGFR at the Alphafold website, and got a .sdf file of Lapatinib at the pdb site....
Leo's user avatar
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4 votes
1 answer
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Average value of lattice parameters from cell trajectory

Is there any post processing tools by which I can get average value of lattice parameters from cell trajectory? For example: I ran 'vc-cp' (CPMD) in quantum espresso (for Silicon) and Si.cel file is ...
Muhammad Hasan's user avatar
3 votes
1 answer
61 views

How to use ASE to combine several MD trajectories into 1 trajectory

I have several continuous MD trajectories. How can I combine them into one trajectory to summarize all?
Binh Thien's user avatar
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2 votes
0 answers
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Convergence issue of Temperature Dependent Lattice constant using CPMD

I am trying to find out temperature dependent lattice constant (Silicon) using CPMD (NPT-MD). If I want the lattice parameters at 300 K, should I set temp 300 K in both &cell and &ion card? I ...
Muhammad Hasan's user avatar
3 votes
1 answer
54 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. ...
Rubi Agrawal's user avatar
4 votes
1 answer
57 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, ...
Roshan Shrestha's user avatar
2 votes
1 answer
27 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:
Yersultan's user avatar
3 votes
2 answers
73 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?
Roshan Shrestha's user avatar
5 votes
1 answer
48 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?
Robin's user avatar
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2 votes
0 answers
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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, ...
Lifelong Learner's user avatar
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, ...
Abd-Elazeem Mohamed's user avatar
6 votes
1 answer
104 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 ...
Kratos1611's user avatar
6 votes
1 answer
119 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 ...
uhoh's user avatar
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4 votes
1 answer
119 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 ...
Lukas's user avatar
  • 303
7 votes
1 answer
63 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 ...
li jiwei's user avatar
2 votes
0 answers
69 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, <...
Vladislav Gladkikh's user avatar
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 ...
horlust's user avatar
  • 163
5 votes
1 answer
58 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. ...
Kieran's user avatar
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5 votes
0 answers
33 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 ...
Rubi Agrawal's user avatar
2 votes
1 answer
69 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....
Kieran's user avatar
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3 votes
0 answers
89 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. ...
Kieran's user avatar
  • 773
2 votes
0 answers
59 views

How to use interatomic potential in LAMMPS

This is my input file for the lammps simulation. ...
Kieran's user avatar
  • 773
7 votes
2 answers
216 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: ...
Vladislav Gladkikh's user avatar
8 votes
3 answers
346 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
  • 163
8 votes
5 answers
769 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
  • 730
3 votes
0 answers
23 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
45 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
  • 773
7 votes
2 answers
376 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
99 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
237 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
  • 61
4 votes
0 answers
44 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
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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
  • 773
4 votes
1 answer
88 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
390 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
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 ...
Mike's user avatar
  • 71
5 votes
1 answer
69 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
36 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
79 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
43 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
60 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
103 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

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