Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
380
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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 ...
3
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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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1
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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 ...
- 2,612
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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 ...
3
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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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2
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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 ...
- 443
3
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1
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57
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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 ...
- 919
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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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55
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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, ...
- 1,257
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123
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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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3
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1
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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 ...
1
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0
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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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2
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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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70
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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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LAMMPS error "Two fix ave commands using same compute chunk/atom command in incompatible ways"
I am very new to using LAMMPS. I am trying to obtain some simulations. I was using an older code which had ave/spatial fix style. In the new LAMMPS version it doesn't work so I am switching to ave/...
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Add Lithium to ATB/GROMOS_54A7_ATB ff
I am using the ATB to get the topology of the Li-TFSI salt.
The calculation 1273328 fails since "Atom type 'LI' not currently supported by the ATB."
Is there a fundamental reason why Li is ...
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Temperature damping parameter in lammps [closed]
I need help on how to set Tdamping in MD simulation. In Lammps documentation it is mentioned that the typical value is 100 for nvt, but when I put this value to my ...
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How to do molecular dynamics with different isotopes of the same element?
In this paper, they separated knock-on damage (originating from the collision of the beam electrons with the nucleus of the target atom) from other radiation damage mechanisms (e.g., ionization damage ...
5
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Do "minimum image convention" and "nearest image" talks about the same things?
I am a little bit confused by the terminologies of Molecular Dynamics simulation.
Do "minimum image convention" and "nearest image" talks about the same things?
What is their ...
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2
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What is the difference between a "periodic image" and a "nearest image" in MD simulation?
As far as I understand -
In MD, when a particle or coordinate moves beyond one face of the simulation box, it reappears on the opposite face as if the box were replicated infinitely in all directions....
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How to maintain constant liquid density during AIMD with NPT ensembe?
I have constructed a solid-liquid interface model with water as the liquid phase. During the AIMD simulation, I used the NPT ensemble. However, I noticed that under the NPT ensemble, the entire model'...
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Loading Gromacs Trajectories using ASE (Atomic-Silumation-Environment)
I am trying to study some trajectories generated using Gromacs. I have been given tpr and pdb files of the simulation. What might be the most effective way to load them in ASE? Or is there way to ...
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I was wondering how I should interpret the results of my molecular dynamics simulation
I ran a molecular dynamics simulation using forcite dynamics for polymers on graphene and a drug. The dynamics summary shows the total energy, potential energy,kinetic energy, total enthalpy, ...
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Classical MD Simulation for mineralization process
I'm currently trying to simulate the calcium carbonate mineralization process on the surface of nanoparticles. In here, I've already borrowed the classical force-field parameters on here(https://pubs....
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How may I make a slab surface to calculate a thin layer with Quantum ESPRESSO?
I want to know how to calculate the band structure and DOS of a thin layer of iron selenide in quantum espresso. How I can fix the input file? Is it different from Bulk matter or the same? Which ...
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What is the largest number of collective variables used in a metadynamics simulation?
Metadynamics is usually used to construct 1D or 2D free-energy surfaces. There seem to be a few examples for 3D free-energy surfaces:
Paper 1: Exploring the Free Energy Landscape of Solutes Embedded ...
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How to choose between Molecular Dynamics and Monte Carlo when beginning to simulate either equilibrium or non-equilibrium systems?
Answers to Are MD and MC both able to study both equilibrium and non-equilibrium systems? include lots of examples pointing to "yes".
I'm currently faced with a task of modelings small ...
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Are MD and MC both parts of statistical physics?
Are MD (Molecular Dynamics) and MC (Monte Carlo) both parts of statistical physics or is only one of them?
If so, which branch (e.g., mechanics, thermodynamics, etc.) and why?
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Are MD and MC both able to study both equilibrium and non-equilibrium systems?
As far as I understand, a system in equilibrium is which already reached its equilibrium state. And, a non-equilibrium system is which hasn't reached its equilibrium state yet.
Are MD (Molecular ...
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Issues simulating the shape transition of silicon clusters using LAMMPS
I have been trying to write an input file for lammps to simulate the shape transition of a nanoparticle of silicon using multiple potentials to obtain the best structure, which I will compare with a ...
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Interaction energy of two cartesian quadrupoles?
I am looking for a complete description of the interaction of two traceless cartesian quadrupoles. Even just an implementation online would be quite useful. The problem I am having is many of the ...
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Parameterizing a Tersoff Potential in LAMMPS
I am seeking advice regarding a molecular dynamics simulation in LAMMPS of Gallium Phosphide (GaP). I came across a paper by Powell et al. which parameterized a tersoff potential for Ga-P interaction, ...
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How to study the stability of structure in water and analyze the radial distribution function (RDF)?
Context:
If I have a system that consists of 20 structures. During molecular dynamics, these structures can form micelles from my point of view.
I would like to do the following:
Confirm if the ...
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What is a 'mover' in molecular dynamics?
Movers
What is a 'mover' in molecular dynamics?
Can you supply me with reading material on 'mover'?
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Unwrapping particle coordinates in MD simulations to remove effects of periodic boundary condition
While calculating various quantities that involves particle positions ( for example, radial distribution function, mean square displacement etc.) using Molecular Dynamics simulation, the effects of ...
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69
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Estimate the time between different residues?
Imagine now, I have 5 structures, and I want to estimate the time when the 5 structures are closer to each other at the same time. I thought I could extract the distance between the different ...
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Looking for the OPLS parameters for octanol
I have been looking for OPLS gromacs parameters for 1-octanol, but haven't been able to get it. Doing a quick web search takes me into links for lipidbook, from which I can't download at all from ...
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NPT Molecular dynamics calculation problem
I am trying to heat up my system from 10K to 300K using the NPT ensemble. But the temperature doesn't reach 300K. What do you think is the problem?
This is my code for the heating part. However, the ...
