12 HPC Tutorials in One Place! From Introductory to Practical, Covering Molecular Simulation/materials Calculation/bioinformatics Analysis and Other Fields
High Performance Computing (HPC) is playing an increasingly important role in scientific research, engineering simulation, artificial intelligence, and big data analysis. It greatly improves computing efficiency through parallel processing and the integration of large-scale computing resources, allowing tasks that originally took days to be completed in hours.
As fields such as computer vision, molecular simulation, material calculation and bioinformatics analysis become increasingly dependent on computing resources, mainstream computing tools such as GROMACS, LAMMPS, VASP and MATLAB have become an important support for scientific researchers to conduct complex simulations and data analysis.
in,GROMACS and LAMMPS are currently the most popular open source tools for molecular dynamics simulations. GROMACS is a high-performance software package for molecular dynamics simulations. With its high-performance computing capabilities and good support for biomolecules, it is widely used in protein dynamics, drug screening and other fields; while LAMMPS is a classic molecular dynamics simulation code that focuses on material modeling. With its flexible modular design and compatibility with multiple force fields, it is favored by researchers in materials science and nanotechnology. This type of open source tool is not only powerful, but also easy to integrate with HPC clusters to facilitate efficient parallel computing.
In comparison,VASP and MATLAB focus more on sophisticated modeling and in-depth analysis in specific scientific research scenarios. VASP is a software focused on first-principles calculations, which is widely used in solid physics and material electronic structure research, and performs well in crystal structure optimization, energy band analysis, etc. MATLAB, with its powerful numerical calculation and visualization capabilities, provides great convenience for scientific research and engineering practice in the fields of image processing, machine learning, engineering simulation, etc.
at present,HyperAI's "Tutorials" section has launched multiple tutorials around the above mainstream tools.From getting started guides to real-world cases, both newbies and experienced researchers/developers can find practical and high-quality resources. Come and experience the power of HPC!
HPC Open Source Tools Tutorial
1. GROMACS Getting Started Tutorial: Lysozyme in Water
Run online:https://go.hyper.ai/K9VVM
This tutorial is an introductory tutorial for molecular dynamics simulations using GROMACS software. Using "lysozyme in water" as an example, you will learn how to prepare and run a typical molecular dynamics simulation of a protein in water.
Run online:https://go.hyper.ai/8wChR
This tutorial is an introductory tutorial for LAMMPS: estimating the melting point of FCC Cu using npt temperature control. You can use the CPU version of LAMMPS to run and experience molecular dynamics simulations.
Run online:https://go.hyper.ai/l1a28
Based on the research data from Nature Medicine in 2024, this tutorial systematically introduces the principles and analysis process of single-cell transcriptome sequencing (scRNA-seq), covering the barcode and UMI mechanisms and their key role in high-precision gene expression analysis.
HPC Professional Research Tools Tutorial
1. VASP Primer: Calculating the Density of States and Energy Bands of Silicon
Run online:https://go.hyper.ai/ZyPGZ
This tutorial is an introductory tutorial on using VASP software for first-principles calculations. Taking "silicon material" as an example, you will learn how to perform structure optimization, state density and energy band calculations.
2. VASP hybrid functional calculation of silicon state density and energy band
Run online:https://go.hyper.ai/TCzWp
This tutorial will learn how to use hybrid functionals to calculate silicon energy bands. Hybrid functionals can calculate the energy bands and state density of materials with correct band gaps, but they require more computing resources, so this tutorial will use a GPU for demonstration.
3. VASP: Molecular dynamics in the NVT ensemble
Run online:https://go.hyper.ai/8EPQH
This tutorial demonstrates molecular dynamics simulations in the NVT ensemble and introduces the core command tag of VASP molecular dynamics: NVT. Users can modify the tag as needed to perform molecular dynamics simulations in other ensembles.
4. VASP combined with Phonopy to calculate the specific heat capacity of silicon
Run online:https://go.hyper.ai/RRHNO
This tutorial will use an automated script to demonstrate the calculation process using Phonopy and learn the basic process of specific heat capacity calculation: preparing the perturbation difference supercell structure, calculating the total energy of all structures, calculating the force constant matrix, and calculating the specific heat capacity of silicon based on the force constant matrix.
5. VASP combined with Phonopy to calculate the phonon spectrum of silicon
Run online:https://go.hyper.ai/pgvsE
This tutorial will use an automated script to perform a Phonopy demonstration calculation process and learn the basic process of phonon spectrum calculation: prepare a perturbation difference supercell structure, calculate the total energy of all structures, calculate the force constant matrix, and calculate the phonon spectrum based on the force constant matrix.
6. Use VASP for machine learning force field training
Run online:https://go.hyper.ai/DpG4T
This tutorial will take silicon crystal as an example, through NpT ensemble molecular dynamics, to demonstrate how to train the vasp machine learning force field, and learn the basic process of machine learning force field training: prepare molecular dynamics input files, change molecular dynamics and machine learning parameters according to actual conditions, and perform simple verification of the machine learning force field by calculating the phonon spectrum.
7. Image dehazing using MATLAB
Run online:https://go.hyper.ai/9Z7Iz
This tutorial uses the Retinex algorithm to remove fog from images and combines it with GPU acceleration to improve computational efficiency, effectively improving image quality and making the target more clearly visible.
8. Using Matlab to process drone signals based on RFUAV system
Run online:https://go.hyper.ai/SZq2T
This tutorial uses MATLAB to implement the key processes of RFUAV, complete tasks such as data conversion, spectrum visualization, SNR estimation, and segment clipping, and analyze and process the IQ signals of the drone.
9. Nonlinear dynamic response analysis of the Koyna earthquake considering hydrodynamic pressure
Run online:https://go.hyper.ai/HBwqI
This tutorial is the official Abaqus tutorial: Seismic Analysis of Concrete Gravity Dams, which illustrates the typical application of the concrete damaged plasticity material model in evaluating the stability and damage of concrete structures under arbitrary loads.