Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
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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?
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Free energy calculations for lammps
Is there any tutorial or reference available to perform free enegy calculations (umbrella sampling; thermodynamic integration; free energy perturbation; widom's particle insertion method) etc. With ...
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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 ...
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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?
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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 ...
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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....
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What are the appropriate boundary conditions for simulating shear deformation of a screw dislocation in LAMMPS?
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:...
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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 <...
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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 ...
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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 ...
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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 ...
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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?
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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 ...
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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 ...
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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 ...
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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 ...
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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
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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 ...
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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 ...
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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 ...
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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?
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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 ...
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"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 ...
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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 ...
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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 ...
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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
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Where should we compute `Energy` in this listing?
Cross-posted here.
I have the following listing for a barebone MD simulation:
...
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Where should we compute `Trajectory` in this listing?
Cross-posted here.
I have the following listing for a barebone MD simulation:
...
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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:
...
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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 ...
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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 ...
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Is the following description talking about the simulation box or the boundary condition?
Is the following description talking about the simulation box or the boundary condition?
To prevent the argon atoms in the gas phase from running off to
infinity, we enclose the system in a "...
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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 ...
5
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757
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Why are Coulomb interactions modeled with just r, not r squared?
As far as I understand (as a complete beginner to molecular simulation and modelling), Coulomb's law for two atoms i and j is:
$$F=k\frac{q_iq_j}{(r_{ij})^2}$$
(the force is proportional to the ...
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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^{\...
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Effect of temperature on Forcefield parameters in classical molecular dynamics simulations
In classical molecular dynamics simulations of complex molecular systems, the force field (FF) contains information about bonded (bonds, angles, dihedrals and impropers) and non-bonded parameters. It ...
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Adaptive Biasing Force Simulations in NAMD
I have performed an ABF simulation to investigate the binding of a small molecule with a 2D surface using NAMD. The initial simulation was for a scan window of 3 to 15 angstroms of z-projected ...
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Saving forces from ASE Molecular Dynamics calculations
I have run some molecular dynamics calculations with a pretrained machine-learning potential (M3GNet) which uses the ASE MolecularDynamics calculator. My goal is to compare the results (energies and ...
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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,...
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Basic MD in ASE
I am testing ASE with a basic H2 MD simulation.
I am reading the input file from a xyz file (generated with Packmol), I set pbc True .
Then, I relax the system with BFGS and move to NVT and NPT ...
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Order Parameter for Water in an MD Trajectory: Understanding Changes in Oxygen-Oxygen-Oxygen Triplet Angular Distributions
I'm interested in understanding how changes in the oxygen-oxygen-oxygen (O-O-O) triplet angular distribution can provide insights into the order parameter.
In literature, the tetrahedral order ...
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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 ...
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Software for storing information of large number of atomic structures into database file
Say I have a MD trajectory that contains a million snapshots (i.e. a million atomic structures). Each snapshot contains some calculated information (either by DFT or some force field) such as energy, ...
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Clustering Algorithms with Periodic Boundary Conditions
I've been working on a project that involves the clustering of data with periodic boundary conditions. Like simulation of extra-framework water species.
Specifically, I am looking for clustering ...
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Visualising the spatial distribution of water structure using VMD
I am trying to recreate Fig. 5b of this paper
I have a solvated NH4+ in my system and would like to create a similar visualisation for my case.
Can this be generated using VMD? If so could someone ...
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Problem with CP2K running AIMD
I have met serious problem with cp2k running AIMD. I complied CP2K 2023.1 with gcc.9.3.0 and intelmpi. First, I ran the test1.inp file (https://1drv.ms/u/s!AtO91yh6_pLhg51bJVuIJt7N4ZZU7w?e=YtB3ZC) and ...
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Establishing AAs protonation - which software to choose?
I need to establish protonation of aminoacids composing the studied protein. To my knowledge there are H++ and Pdb2pqr servers that are able to do that. However, they yield quite much different ...
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318
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How to build up a supercell for explicit solvent system?
I would like to construct the supercell that contains explicit 4 ionic liquid molecules (i.e. $[EMIM][BF_{4}]$) for running AIMD. Is there any recommended software or code that is suitable and easy to ...
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Analyzing ELECTRO -ELECTROLYTE MD trajectories for calculating bulk density in a simulation box [closed]
I am simulating electrode electrolyte simulation and my professor told me to calculate the density of bulk in simulation box, I am clueless about the how to calculate ,also I want to know if charges ...
7
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Keeping a coarse grained particle off plane (Molecular Dynamics)
I have a coarse-grained particle (bead) that I want to keep off the plane from the plane of other beads which form like a 2D plane. Do people employ improper dihedral for this or any other bonded ...
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