How to Generate Random Initial Configurations for AIMD Simulations of H₂O on...
I am planning to perform AIMD simulations of H₂O on Ni(110) using VASP. For AIMD, I would like to generate multiple independent trajectories with randomized initial conditions.What is the standard...
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Parameters to observe spinodal transition in a molecular dynamics simulation...
I would like to observe the spinodal transition in a molecular dynamics simulation with interacting points and a Lennard Jones potential using the reduced units of the argon atom, and the code provided...
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Why do ionic liquids split during an NVT simulation in GROAMACS?
The confined liquid between two graphene electrodes seems to split during my NVT simulation. as given in the picture.when I do the simulation with just the ionic liquid nothing of this sort happens. I...
View ArticleSimulating glass compositions with molecular dynamics – is using the minimum...
I would like to know if anyone has experience simulating glass compositions for molecular dynamics calculations.As a first step, I took the crystalline bases of the glasses and built a random structure...
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Can you explain PCA?
I saw this picture in MDAnalysis. However, I do not fully understand the shape. The PC1-PC2 plot looks like a convex. For PC1/PC3, it is a Z-shape. For PC2/PC3, it is an alpha-shape. Does the shape...
View ArticleSlab formation of PLA( poly lectic acid)
I want to know how can I make a slab structure of polymers for example polylectic acid(PLA) and where can I find their cif files etc?
View ArticleGood AIMD RMSE but unstable MD; adding distortions breaks TRAIN error without...
I am training MACE on a 10 ps DFT-AIMD trajectory.Although the model shows reasonable RMSE on AIMD data, MD with the trained MACE potential is unstable (structure distortion and temperature blow-up)....
View ArticleNano scratching wear mechanism by lammps
I'm currently doing materials simulation on Molecular Dynamics. I want to implement wear mechanism script. Where I created my simulation structure like this substrate of Fe and Diamond indenter by...
View ArticleGPCR simulation into triclinic box
I am trying to simulate a GPCR complex embedded in a membrane within a triclinic box prepared using CHARMM-GUI with Amber.I am encountering an issue when attempting to run Amber with ntp=3...
View ArticleMinimum-image convention and spherical cutoff
When simulating systems with periodic boundary conditions, it is a standard practice to avoid calculating interactions with all possible images of the particles and instead pick the closest image. For...
View ArticleModeling vibronic interaction beyond Born-Oppenheimer
Within Born-Oppenheimer approximation, the motion of atomic nuclei are considered as being separated from the electrons movement. Although in general this approximation is valid for a high number of...
View ArticleRestarting AIMD Simulation from an Interrupted Run: Resolving WAVECAR...
I'm running an AIMD simulation for a system, and I need to simulate for 20 ps. However, the simulation stops after only 2 ps, and I need to continue it from this point using the WAVECAR generated in...
View ArticlePerforming two (restrained and unrestrained) NVT and two (restrained and...
Do I need to edit position restrain file for both protein and ligand manually, or may I perform changing parameter "define" from NVT.mdp and NPT.mdp files? Total number of atoms before simulation is...
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Include Li+ in force field for Molecular Dynamics
I want to perform some MD including Li+ ions. Specifically I am interested in Li-TFSI (aka Lithium bis(trifluoromethanesulfonyl)imide).I tested both the ATB repository and LigParGen and neither can...
View ArticleLAMMPS binary mixture simulation
I am doing a simple binary mixture simulation in LAMMPS where I want to see first how phase separation occurs for later introducing active particles. My concern is that I am setting the interactions of...
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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...
View ArticleCalculating errors/uncertainty when finding the self-diffusion coefficient of...
I am looking at the temperature dependence of self-diffusion coefficient of water using SPC model in gromacs. GROMACS reports an error with the diffusion coefficient. What exactly is this error? Is it...
View ArticleRestarting MD calculation in Quantum Espresso with different Npool
I’m running some AIMD calculations in Quantum Espresso and using max_seconds in my job script to restart the runs on the cluster. I’m currently using 14 k-points and have set -npool to 14 in the...
View ArticleVirial stress interaction counting
I am trying to measure the virial stress tensor in a subset of a larger simulation box. Since I am not measuring the stress for the whole system, I have to decide what to do with the forces between...
View ArticleAs a beginner in Computational Chemistry field,which configuration computer...
I am a undergrade students in chemistry major, I have great ambitions in Computational chemistry field.I want to do M.Sc and furthermore in this field.I want prepare myself for this from today.I want...
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