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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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Error with running GROMACS with SLURM [closed]

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
81 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
25 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
196 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
91 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
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3 votes
1 answer
142 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
  • 1,637
4 votes
1 answer
43 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
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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
269 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
144 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
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6 votes
0 answers
117 views

Why is potential energy used and not total energy when calculating free energy? [closed]

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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2 votes
0 answers
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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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2 votes
1 answer
50 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
102 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
126 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
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4 votes
0 answers
185 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
185 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
117 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
216 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
41 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
2 votes
1 answer
73 views

Is there a way to force GROMACS to keep a certain density for water?

I am trying to fully populate my GROMACS simulation, but the water density in the bulk is too low. Here are the steps I used: Add organic monolayer into 9x9x9 box Solvate with water equilibrate t-...
Peter Yang's user avatar
3 votes
1 answer
63 views

Exclusion of Lennard-Jones potential between O-H and H-H in water models

In reading Jorgensen's 1983 paper comparing the properties of 6 water models it was mentioned that there is the inclusion of an L-J potential between pairs of oxygen molecules, but no mention of ...
KashmirWalla's user avatar
2 votes
1 answer
253 views

Absorption enthaply at different temprature in VASP software via ab initio molecular dynamics

Can we calculate the absorption enthalpy at different temperature in VASP software via ab initio molecular dynamics? If yes, how?
Rubi Agrawal's user avatar
1 vote
0 answers
114 views

Free energy calculations for lammps

Is there any tutorial or reference available to perform free energy calculations (umbrella sampling; thermodynamic integration; free energy perturbation; wisdom's particle insertion method) etc. with ...
Robin's user avatar
  • 61
3 votes
0 answers
39 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
0 answers
25 views

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
1 vote
1 answer
52 views

When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?

Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled ...
Don Aborah's user avatar
3 votes
1 answer
60 views

Adsorption of Li on GeC (optimization problem)

Actually I am trying to study the adsorption of Li or K on the sheet starting from the hexagon centre the system optimises with Li or (K) adsorbed over one of the Ge atoms and not remain at the centre....
Mas's user avatar
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1 vote
0 answers
35 views

What are the appropriate boundary conditions for simulating shear deformation of a screw dislocation in LAMMPS? [closed]

I'm seeking clarification on the selection of suitable boundary conditions for simulating shear deformation of a screw dislocation using LAMMPS. In my script, I currently employ the following commands:...
Vikram Roy's user avatar
3 votes
0 answers
219 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
1 vote
1 answer
250 views

Issue building deepmd kit for a plugin version of LAMMPS

I am following the deepmd-kit documentation to implement this kit into a plugin version of LAMMPS, the documentation I am using is found here and here. I am close to completing everything, but am ...
Baba Booey's user avatar
4 votes
0 answers
65 views

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
4 votes
0 answers
115 views

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
3 votes
2 answers
129 views

Adsorption of naphthalene on graphene oxide sheets with gmx

How to set up a molecular dynamics (MD) simulation for the adsorption of naphthalene on graphene oxide sheets using GROMACS?
Mohamed El-amine's user avatar
4 votes
1 answer
234 views

ASE: Shape mismatch when using FrechetCellFilter filter

I want to use a FrechetCellFilter into a MD simulation with ASE to make sure both the atomic forces and unit cell are simultaneously minimised. I encounter a ...
Marco Di Gennaro's user avatar
3 votes
0 answers
48 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
9 votes
0 answers
119 views

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
  • 453
9 votes
2 answers
196 views

Berendsen thermostat: why are the two time constants not equal?

With reference to the GROMACS manual 2023.2, the discussion of the Berendsen thermostat (p. 362) indicates that the time constant $\tau$ which governs the steepness of the relaxation toward a target ...
KashmirWalla's user avatar
3 votes
0 answers
107 views

I need molecular dynamics simulations input file for hexagonal heterostructures in quantum espresso [closed]

I m a material science student of PhD and search alot and make some input files for AIMD simulation but I didn't get the best output if anyone have the input file please provide me
Umair Khan 's user avatar
2 votes
0 answers
59 views

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
  • 2,546
5 votes
2 answers
155 views

How is the equation for the position of a virtual site derived?

Cross posted on Math SE I am trying to understand virtual sites in MD simulations, and I came across this configuration: Here, coordinate $\mathbf{s}$ represents the virtual site, which is formed by ...
Vasista's user avatar
  • 1,341
-4 votes
1 answer
101 views

Are these simulator, visualizer, or force field? [closed]

I see that some "names" are available online in relation to MD simulation. VMD NAMD LAMMPS OpenMM GROMACS Amber CHARMM Are these "names" simulators, visualizers, force fields, or ...
user366312's user avatar
  • 2,546
6 votes
3 answers
996 views

Which MD software is preferable for protein simulation?

I see that some free MD simulation software are available online. VMD NAMD LAMMPS OpenMM GROMACS Amber CHARMM Which one above is the most appropriate for protein simulation?
user366312's user avatar
  • 2,546
4 votes
0 answers
63 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
  • 41
3 votes
1 answer
269 views

"ERROR: Lost atoms" while simulating N2/CO2 mixture

I am trying to simulate a mixture of CO2 and N2 but I keep getting ERROR: lost atoms: original 1500 current 1495. I have performed several energy minimizations and ...
Michael Anokye's user avatar
2 votes
0 answers
189 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
4 votes
0 answers
50 views

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
3 votes
1 answer
400 views

Finding the total energy using quantum espresso

I am a beginner in Quantum Espresso When I want to calculate the total energy for Cu for example, I write the input file for primitive cell or conventional cell, what is the difference? Thank you
user307903's user avatar

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