Π£ Π½Π°Ρ Π²Ρ ΠΌΠΎΠΆΠ΅ΡΠ΅ ΠΏΠΎΡΠΌΠΎΡΡΠ΅ΡΡ Π±Π΅ΡΠΏΠ»Π°ΡΠ½ΠΎ Molecular Dynamics Simulation with GROMACS: A Beginner's Tutorial ΠΈΠ»ΠΈ ΡΠΊΠ°ΡΠ°ΡΡ Π² ΠΌΠ°ΠΊΡΠΈΠΌΠ°Π»ΡΠ½ΠΎΠΌ Π΄ΠΎΡΡΡΠΏΠ½ΠΎΠΌ ΠΊΠ°ΡΠ΅ΡΡΠ²Π΅, Π²ΠΈΠ΄Π΅ΠΎ ΠΊΠΎΡΠΎΡΠΎΠ΅ Π±ΡΠ»ΠΎ Π·Π°Π³ΡΡΠΆΠ΅Π½ΠΎ Π½Π° ΡΡΡΠ±. ΠΠ»Ρ Π·Π°Π³ΡΡΠ·ΠΊΠΈ Π²ΡΠ±Π΅ΡΠΈΡΠ΅ Π²Π°ΡΠΈΠ°Π½Ρ ΠΈΠ· ΡΠΎΡΠΌΡ Π½ΠΈΠΆΠ΅:
ΠΡΠ»ΠΈ ΠΊΠ½ΠΎΠΏΠΊΠΈ ΡΠΊΠ°ΡΠΈΠ²Π°Π½ΠΈΡ Π½Π΅
Π·Π°Π³ΡΡΠ·ΠΈΠ»ΠΈΡΡ
ΠΠΠΠΠΠ’Π ΠΠΠΠ‘Π¬ ΠΈΠ»ΠΈ ΠΎΠ±Π½ΠΎΠ²ΠΈΡΠ΅ ΡΡΡΠ°Π½ΠΈΡΡ
ΠΡΠ»ΠΈ Π²ΠΎΠ·Π½ΠΈΠΊΠ°ΡΡ ΠΏΡΠΎΠ±Π»Π΅ΠΌΡ ΡΠΎ ΡΠΊΠ°ΡΠΈΠ²Π°Π½ΠΈΠ΅ΠΌ Π²ΠΈΠ΄Π΅ΠΎ, ΠΏΠΎΠΆΠ°Π»ΡΠΉΡΡΠ° Π½Π°ΠΏΠΈΡΠΈΡΠ΅ Π² ΠΏΠΎΠ΄Π΄Π΅ΡΠΆΠΊΡ ΠΏΠΎ Π°Π΄ΡΠ΅ΡΡ Π²Π½ΠΈΠ·Ρ
ΡΡΡΠ°Π½ΠΈΡΡ.
Π‘ΠΏΠ°ΡΠΈΠ±ΠΎ Π·Π° ΠΈΡΠΏΠΎΠ»ΡΠ·ΠΎΠ²Π°Π½ΠΈΠ΅ ΡΠ΅ΡΠ²ΠΈΡΠ° ClipSaver.ru
This step-by-step tutorial is designed for beginners who want to learn how to set up and run molecular dynamics (MD) simulations using GROMACS. This video will not just show the process; I will explain each step and the reasons behind it. Furthermore, I will discuss GROMACS's input and output files. This video is part of the online GROMACS workshop hosted by InsilicoSci. Participate in the workshop: https://bit.ly/41TytXj To get the simulation parameter files click on this link: https://bit.ly/3LVCTrc Outlines 00:14 Introduction 00:56 How to find protein structures 03:24 Introducing the PDB file format 05:07 Visualise a protein structure using VMD 05:46 Remove water molecules from the structure 07:43 Explaining the GROMACS input flowchart 11:37 Fixing missing atoms in PDB files 13:22 Create a topology file for a protein structure 15:24 Explaining the GROMACS coordinate file (gro) 16:13 Explaining the GROMACS topology file 19:37 Remove GROMACS backup files 20:06 Setting up a PBC box 23:11 Adding solvent molecules to the simulation box 25:00 Adding ions 28:43 Minimising system 34:10 Equilibrating system in the NVT ensemble 36:01 Explaining position restraints in GROMACS 38:28 Explaining the GROMACS MDP file 45:01 How to check if the system reached equilibrium 47:09 Equilibrating system in the NPT ensemble 51:59 Performing the product simulation 52:49 Explaining GROMACS compressed and uncompressed trajectory files 55:05 Explaining GROMACS output files 56:14 How to restart and extend a simulation 01:00:35 Visualise and check trajectory files using VMD 01:03:19 Performing basic analysis of simulation results 01:04:44 RMSD analysis 01:07:12 Radius of gyration analysis insilicosci.com