Question about VACF from MD simulation
I have several LAMMPS NVT MD simulations at several different constant temperatures, for some crystals and amorphous materials, all of them are 3D periodic bulk system. All of them have 10k iterations....
View ArticleHow can I restart a job in VASP software?
I'm running an AIMD (Ab initio molecular dynamics) calculation in the NVE ensemble with a specific initial kinetic energy (without using temperature control). My job stopped before the simulation time...
View ArticleBackmapping problem from martini to charmm36
I have been reverse mapping successfully until a week ago. backward.py is confusing atoms for different residues for another. For example, it confuses atoms for met for ala, some cases, asp for arg....
View ArticleError in VMD when trying to visualize MD trajectory
I am trying to load a trajectory, in the form of a .trj file into VMD. VMD loads my inital .xyz molecule fine. But when I try to load into the molecule my .trj file (with Gromacs TRJ trajectory file...
View ArticleHow compute system dynamics from the solution of the Schrödinger equation?
As I understand the main problem of matter modeling is that for atoms and molecules larger than a hydrogen atom it is very difficult to find a solution to the Schrödinger equation. Let us assume that...
View ArticleHow to identify the relationship between stability and local chemical...
Are there any physical quantities that can characterize the local chemical environment of surfaces with different orientations? I have found that different facets in my system have varying stabilities...
View ArticleHow to parameterize force field for a transition metal complex
It is a general question. I know, but I need some help.I am interested to parametrize a complex that contains transition metal like Ru and Pt etc.Furthermore, I will use this Force Field to do...
View ArticleSwitching Amber Versions Mid-Project
Background: I have been running a large number of MD simulations in in the 2022 build of Amber for the last two years, as it is what I had available on my local supercomputer center. Recently, that...
View ArticleHow is Radius of Gyration Calculated by Amber's CPPTraj
Background: I have a simulation of a long string-like molecule anchored at both ends. I am trying to use the radgyr function in the Amber CPPTraj utility to get the non-mass-weighted 3D radius of...
View ArticleWhy Does the Unit Cell Change During My SIESTA Calculation
I am performing calculations using SIESTA, and I noticed that the unit cell dimensions are changing during the simulation. Could someone please help me understand why this is happening and how to...
View ArticleHow 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...
View ArticleInquiry About Missing Al-Al, P-P, and Al-P Potentials in Buckingham Potential...
I am currently working on the AlPO4 system and attempting to reproduce data from the paper https://doi.org/10.1080/08927029608024086. However, I have encountered an issue regarding the availability of...
View ArticleUnwrapping while using Dislocation Analysis Algorithm (DXA) in Ovito Python...
I'm currently trying to measure the glide velocity of dislocations using LAMMPS and Ovito. I have performed a simulation where I apply a shear stress to my simulation box, making the dislocation move....
View ArticleReplicating thermal conductivty measurments from MD paper
I'd like to replicate the results from this paper: https://doi.org/10.1103/PhysRevB.80.165203But I've had some issues as of now. The paper describes their set up as: 'A fully relaxed structure has...
View ArticleClustering 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...
View ArticleWhat exactly is an integrator?
I just finished the basic OpenMM tutorial "Protein in Water" and it works and all but I am feeling quite lost. What exactly is an integrator?
View ArticleMolecular dynamics in understanding the structure of a given protein
I still haven't started with MD simulations. I am interested in understanding the molecular mechanism of water permeability through protein channels. Can MD help in this regard ?
View ArticleCP2K: How to Define a Molecule and Restrict Lennard-Jones Interactions Within...
I am trying to simulate molecular dynamics for a hypothetical chain of carbon atoms (this is a minimum working example designed to illustrate a larger issue I am facing). Each molecule consists of 5...
View ArticleHow can be the radius of the atom determined from the RDF?
I have been wondering how one can determine the atomic radius from the radial distribution function (RDF) of a specific type of atom. Let's say I have a liquid argon system and generate the RDF from a...
View ArticleUse MDAnalysis for trajectory
I'd like to use MDAnalysis. But I have diffusion.traj file only. MDAnalysis requires a topology file, which contains information about bondings, charges, etc, as I found in MDAnalysis guideline....
View ArticleMolecular dynamics with multiple timesteps
I am trying to write a molecular dynamics code where the system can be separted into two fragments/parts.Are there any known receipes to use different propagators and timesteps for different fragments...
View ArticleModified Verlet algorithm
I have been looking at a publication on Dissipative Particle Dynamics (Groot, Rob & Warren, Patrick. (1997). Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic...
View ArticleAssessing the Transferability of a Machine Learning Force Field (MLFF) for...
I have trained a machine learning force field (MLFF) on a relatively small system and evaluated its performance by comparing key transport properties with direct AIMD calculations. For a small system...
View ArticleHow to understand pressure fluctuations and volume changes in molecular...
I am performing molecular dynamics (MD) simulations to melt a silicon crystal (32,000 atoms) using the Tersoff potential in LAMMPS. My goal is to achieve a disordered liquid system for subsequent...
View ArticleIs there a scripted tool to add neutral terminal caps (e.g. NME, ACE) to...
I have a range of systems consisting of multiple peptide chains, some of which are one residue (i.e. single amino acids), which I'd like to analyse using molecular dynamics and AMBER-flavour...
View ArticleStandard experimental data for comparison of simulation results
I'm simulating gaseous nitrogen with molecular dynamics simulations. I want to make sure that the pair-potential I use is accurate. Is there any database where I can get accurate values of some...
View ArticleHow to write a LAMMPS dump command compatible with ASE that includes forces...
I am using LAMMPS and want to write a dump command that outputs atomic positions, forces, and total energy in a format that ASE (Atomic Simulation Environment) can read and attach a...
View ArticleBest practices for statistical error estimation in molecular dynamics
I'm performing a molecular dynamics (MD) simulation of a system of particles in a harmonic oscillator, trying to calculate its average kinetic energy. The exact kinetic energy is known from theoretical...
View ArticleWhat does "200 nanoseconds of simulation" mean?
I have begun studying molecular dynamics, but some concepts still confuse me.For instance, when I encounter the phrase "The simulation ran for 200 ns," I am puzzled by its meaning. What does 200 ns of...
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Why does the temperature fluctuate severely during the AIMD using an NVT...
I am trying to raise the temperature of my model and keep the temperature at 300K, with an NVT ensemble and Nose-Hoover thermostat. I am doing this job with VASP, here is the INCAR file.DFT+U...
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