🎯 Key Takeaways for quick navigation: 00:00 🎙️ *Introduction and Collaboration Overview* - Introduction to the molecular dynamic simulation webinar. - Overview of the collaborating institution, Data Science by Informatics, and its expertise. 02:36 🌐 *Services Offered by Data Science by Informatics* - Expertise in structural bioinformatics, genomic sequences, transcriptomic services, AI/machine learning, and consultancy/training services. - Emphasis on providing details and assistance in structural bioinformatics. 03:17 👨🏫 *Guest Introduction and Opening Remarks* - Introduction of Professor Dr. Mahmoud Ashraf, a collaborator and expert in various scientific domains. - Acknowledgment of Professor Ashraf's contributions and expertise. 04:13 🧪 *Focus on Molecular Dynamics Simulations* - Overview of the webinar's focus on molecular dynamics simulations. - Emphasis on practical demonstrations, specifically using Gromacs software. 04:42 🖥️ *Gromacs as a Benchmark Software* - Recognition of Gromacs as a benchmark software for molecular dynamics simulations. - Preference for open-source software like Gromacs due to flexibility. 05:40 🤔 *Understanding Molecular Dynamic Simulations* - Conceptual explanation of molecular dynamics simulations. - Discussion on the dynamic nature of atoms, introducing the idea of movement and kinetic energy. 06:48 ⚛️ *Types of Atom Interactions* - Explanation of various interactions: covalent, ionic, van der Waals, and hydrogen bonds. - Emphasis on understanding the dynamic nature of atoms, even in seemingly static structures. 13:01 📉 *Calculating Force in Molecular Dynamics* - Illustration of the relationship between interaction energy and atomic distance. - Explanation of how interaction energy helps calculate the force between atoms. 16:12 📚 *Newton's Second Law in Molecular Dynamics* - Application of Newton's second law (Force = mass × acceleration) in molecular dynamics simulations. - Connection between force, mass, and acceleration in predicting atom positions. 20:40 🕰️ *Importance of Nanoseconds in Molecular Dynamics Simulations* - The behavior of biological molecules occurs at the nanoseconds or femtoseconds level. - Enzymes and proteins involved in physiological actions operate at picoseconds or femtoseconds. - Preparation of the protein structure is the initial step in molecular dynamics simulations. - Subsequent steps include preparing the protein topology file, solvating and ionizing the system, energy minimization, equilibration, production, and analysis. 26:18 🧬 *Preparation of 3D Protein Structure* - Obtaining a realistic 3D structure of the molecule is crucial for accurate simulations. - Protein Data Bank (PDB) and AlphaFold are two sources for obtaining 3D protein structures. 32:48 🛢️ *Role of Force Fields in Topology File Preparation* - Force fields are mathematical descriptors used to model atomic interactions in molecules. - Gromacs provides default force fields such as OPLS, Amber, and CHARMM. 38:08 ⚗️ *Solvation and Ionization in Molecular Dynamics* - Solvation involves placing the protein in a water box to simulate a natural, hydrated environment. - Ionization is crucial to maintain a neutral environment, mimicking natural cellular conditions. 39:44 📉 *Energy Minimization in Molecular Dynamics* - Energy minimization is essential to bring molecules to their lowest energy state, ensuring stability. - Unstable molecules are prone to high energy states, leading to potential inaccuracies in simulations. 40:57 🧬 *Protein Stability and Energy Minimization* - Proteins need to be stable before molecular dynamics simulation. - Stabilization involves minimizing the protein's energy, commonly done using the steepest descent method. 42:41 🔄 *Equilibration Process after Energy Minimization* - Equilibration involves relaxing the entire system after energy minimization. - Two types of equilibration: NVT (controlling temperature) and NPT (controlling pressure). 44:21 ⚖️ *Selecting Force Fields for Different Molecules* - Force field selection depends on the molecule type (protein, organic molecule, lipid, nucleation). - Different force fields are designed for specific molecular categories. 45:41 🧪 *Adding Ions for System Ionization* - Sodium, potassium, and chloride ions are added to achieve system ionization. - Ionization aims to create a neutral system in a natural environment. 47:04 📚 *Validating Force Field Constants through Literature Review* - Validating force field constants involves a thorough literature review. - Checking if the force field was designed for a similar molecule. 01:01:18 📊 *Protein Conformation and Dynamics* - Demonstrates the change in protein conformation over time using a radius graph. - Discusses the significance of monitoring protein conformation changes through graphs. 01:04:24 🌐 *Introduction to Bioinfo Experts* - Introduces Bioinfo Experts, a platform sharing knowledge on bioinformatics and molecular dynamics. - Describes their journey from starting a TH-cam channel to extending to Udemy and Fiverr. 01:06:02 💡 *Bioinfo Experts Courses and Achievements* - Showcases Bioinfo Experts' courses on Udemy related to bioinformatics and molecular dynamics. - Shares QR codes for easy access to their courses and offers private consultancy. 01:07:50 🏆 *Recognition and Certificates* - Emphasizes the global reach of Bioinfo Experts' courses with participants from various regions. - Shares recommendations and testimonials from satisfied students. 01:08:31 🖥️ *Practical Demonstration Preparation* - Prepares for a practical demonstration of molecular dynamics simulation using Gromacs. 01:11:57 💻 *Installing Gromacs on Windows (WSL)* - Guides on installing Gromacs on Windows using Windows Subsystem for Linux (WSL). 01:16:11 ⚙️ *Preparing Topology File with Gromacs* - Demonstrates using the `pdb2gmx` module to generate a topology file. 01:21:31 🎉 *Successful Topology File Generation* - Verifies the successful execution of the `pdb2gmx` command. 01:21:46 📁 *Setting Up Topology File* - Overview of creating a topology file for molecular dynamics simulation. 01:23:20📦 Solvation *Process (Part 1)* - Initiating the solvation process by creating a box around the protein. 01:25:39 🚰 *Solvation Process (Part 2)* - Continuing the solvation process by adding water molecules to the box. 01:27:33 ⚡ *Ionization Process* - Introduction to the ionization step in molecular dynamics simulation. 01:30:58 🌐 *Preparing TPR File for Energy Minimization* - Utilizing the "grompp" module to generate the TPR file for energy minimization. 01:37:26 ⚙️ *Energy Minimization* - Initiating the energy minimization process using the "mdrun" module. 01:39:04 🛠️ *Commercial Services and Q&A Announcement* - Brief overview of commercial services related to MD simulation. 01:42:14 🔧 *Creating tpr File for NBT Calibrations* - Demonstrated the process of creating a tpr file for NBT calibrations using Gromacs. 01:44:01 🤔 *Troubleshooting NVT File Selection* - Identified an issue with the NVT file selection for ligand-protein simulations. 01:44:46 ⚙️ *Initiating Energy Minimization and NBT Preparation* - Successfully created the tpr file for NBT preparation after resolving the selection issue. 01:45:55 🚀 *Simulation Results and Setup Overview* - Shared pre-fetched results, including graphs for area, gyration, hydrogen bonds, RMSD, and RMSF. 01:46:52 🖥️ *Overview of Supercomputing Facility and Collaboration* - Acknowledged the collaboration with a supercomputing facility (RTX 149t) for academic activities. 01:48:31 📂 *Understanding and Modifying MDP Files* - Explored the content of the MDP (molecular dynamics parameter) file, focusing on the "nsteps" parameter. 01:51:18 📊 *Analyzing RMSD Results Using Excel* - Shared how to open and analyze RMSD files using Excel for understanding protein stability. 01:54:34 🤝 *Q&A Session: Answering Participant Questions* - Addressed participant questions regarding missing residues, repairing protein structures, and solvation necessity. 02:00:39 🧪 *Exploring Drug-Protein Interactions* - Responded to a participant question about assessing drug-protein interaction strength. 02:03:20 🌐 *Exploring Non-Covalent Interactions in Molecular Systems* - Addressed a question from a participant with a physical chemistry background. 02:04:43 🎨 *Molecular Structure Drawing* - Drawing three-dimensional molecular structures using software like ChemDraw, Material Studio, or ChemSketch. 02:05:39 🧪 *Force Field Selection and Preparation* - Decide the appropriate force field based on the molecule's nature. 02:08:50 🔍 *Spectroscopy Properties and Gromacs Modules* - Install Gromacs modules for specific spectroscopy properties like Raman effect. 02:12:23 ⚙️ *Topology Error Resolution in PDB2GMX* - Use `-ignh` option to ignore topology errors for one or two amino acid residues. 02:16:07 ⏱️ *Accelerating MD Simulations* - For faster MD simulations, seek external bioinformatics services. Made with HARPA AI
Nice webinar! The instructions are clear and easy to follow. As a suggestion for future webinars, to avoid background noise, the host could keep his mic muted while the speaker is talking.
Thanks for the impactful lecture. My questions are: 1. How do you know if the system's energy is minimized to be bearest? 2. How do you know if the system is completely relaxed?
You can check if the system's energy is minimized by observing the potential energy during the energy minimization process. In GROMACS, after running the energy minimization, you can use the gmx energy tool to analyze the energy minimization log file (.log). Look at the potential energy (Potential) and ensure it reaches a stable minimum value. A system is considered completely relaxed when it has equilibrated, meaning the properties of the system are stable over time. You can check this by running an equilibration simulation and then analyzing key properties such as temperature, pressure, and density. In GROMACS, you can use the gmx energy tool to extract these properties from the .edr file:
It's not necessary for the NVT, NPT, and MD production times to be the same. Typically, NVT and NPT are equilibration steps, where you allow the system to stabilize at the desired temperature (NVT) and pressure (NPT) before running the production MD simulation. The equilibration time (NVT and NPT) is often shorter than the production MD simulation, which can be run for a longer period to gather sufficient statistical data. So, you can have shorter NVT and NPT phases, and a longer final MD production run. The key is ensuring that the system is well-equilibrated before starting the production MD.
When i use "gmx2pdb -f x.pdb ... NOw, i m getting a warm : "Fatal error: Residue 'UNK' not found in residue topology database." then when I delete the UNK part in pdb file.. there is no warm and error from this code. how to solve this problem while the "gmx2pdb -f ....." is used without not delete the ligands from the pdb file?..thanks
Does anyone have the chrmm file that we need to download from Mackerell website???...the website server is down nowadays..and I need to perform an MD simulation for my research project...Please respond..if anyone have
🎯 Key Takeaways for quick navigation:
00:00 🎙️ *Introduction and Collaboration Overview*
- Introduction to the molecular dynamic simulation webinar.
- Overview of the collaborating institution, Data Science by Informatics, and its expertise.
02:36 🌐 *Services Offered by Data Science by Informatics*
- Expertise in structural bioinformatics, genomic sequences, transcriptomic services, AI/machine learning, and consultancy/training services.
- Emphasis on providing details and assistance in structural bioinformatics.
03:17 👨🏫 *Guest Introduction and Opening Remarks*
- Introduction of Professor Dr. Mahmoud Ashraf, a collaborator and expert in various scientific domains.
- Acknowledgment of Professor Ashraf's contributions and expertise.
04:13 🧪 *Focus on Molecular Dynamics Simulations*
- Overview of the webinar's focus on molecular dynamics simulations.
- Emphasis on practical demonstrations, specifically using Gromacs software.
04:42 🖥️ *Gromacs as a Benchmark Software*
- Recognition of Gromacs as a benchmark software for molecular dynamics simulations.
- Preference for open-source software like Gromacs due to flexibility.
05:40 🤔 *Understanding Molecular Dynamic Simulations*
- Conceptual explanation of molecular dynamics simulations.
- Discussion on the dynamic nature of atoms, introducing the idea of movement and kinetic energy.
06:48 ⚛️ *Types of Atom Interactions*
- Explanation of various interactions: covalent, ionic, van der Waals, and hydrogen bonds.
- Emphasis on understanding the dynamic nature of atoms, even in seemingly static structures.
13:01 📉 *Calculating Force in Molecular Dynamics*
- Illustration of the relationship between interaction energy and atomic distance.
- Explanation of how interaction energy helps calculate the force between atoms.
16:12 📚 *Newton's Second Law in Molecular Dynamics*
- Application of Newton's second law (Force = mass × acceleration) in molecular dynamics simulations.
- Connection between force, mass, and acceleration in predicting atom positions.
20:40 🕰️ *Importance of Nanoseconds in Molecular Dynamics Simulations*
- The behavior of biological molecules occurs at the nanoseconds or femtoseconds level.
- Enzymes and proteins involved in physiological actions operate at picoseconds or femtoseconds.
- Preparation of the protein structure is the initial step in molecular dynamics simulations.
- Subsequent steps include preparing the protein topology file, solvating and ionizing the system, energy minimization, equilibration, production, and analysis.
26:18 🧬 *Preparation of 3D Protein Structure*
- Obtaining a realistic 3D structure of the molecule is crucial for accurate simulations.
- Protein Data Bank (PDB) and AlphaFold are two sources for obtaining 3D protein structures.
32:48 🛢️ *Role of Force Fields in Topology File Preparation*
- Force fields are mathematical descriptors used to model atomic interactions in molecules.
- Gromacs provides default force fields such as OPLS, Amber, and CHARMM.
38:08 ⚗️ *Solvation and Ionization in Molecular Dynamics*
- Solvation involves placing the protein in a water box to simulate a natural, hydrated environment.
- Ionization is crucial to maintain a neutral environment, mimicking natural cellular conditions.
39:44 📉 *Energy Minimization in Molecular Dynamics*
- Energy minimization is essential to bring molecules to their lowest energy state, ensuring stability.
- Unstable molecules are prone to high energy states, leading to potential inaccuracies in simulations.
40:57 🧬 *Protein Stability and Energy Minimization*
- Proteins need to be stable before molecular dynamics simulation.
- Stabilization involves minimizing the protein's energy, commonly done using the steepest descent method.
42:41 🔄 *Equilibration Process after Energy Minimization*
- Equilibration involves relaxing the entire system after energy minimization.
- Two types of equilibration: NVT (controlling temperature) and NPT (controlling pressure).
44:21 ⚖️ *Selecting Force Fields for Different Molecules*
- Force field selection depends on the molecule type (protein, organic molecule, lipid, nucleation).
- Different force fields are designed for specific molecular categories.
45:41 🧪 *Adding Ions for System Ionization*
- Sodium, potassium, and chloride ions are added to achieve system ionization.
- Ionization aims to create a neutral system in a natural environment.
47:04 📚 *Validating Force Field Constants through Literature Review*
- Validating force field constants involves a thorough literature review.
- Checking if the force field was designed for a similar molecule.
01:01:18 📊 *Protein Conformation and Dynamics*
- Demonstrates the change in protein conformation over time using a radius graph.
- Discusses the significance of monitoring protein conformation changes through graphs.
01:04:24 🌐 *Introduction to Bioinfo Experts*
- Introduces Bioinfo Experts, a platform sharing knowledge on bioinformatics and molecular dynamics.
- Describes their journey from starting a TH-cam channel to extending to Udemy and Fiverr.
01:06:02 💡 *Bioinfo Experts Courses and Achievements*
- Showcases Bioinfo Experts' courses on Udemy related to bioinformatics and molecular dynamics.
- Shares QR codes for easy access to their courses and offers private consultancy.
01:07:50 🏆 *Recognition and Certificates*
- Emphasizes the global reach of Bioinfo Experts' courses with participants from various regions.
- Shares recommendations and testimonials from satisfied students.
01:08:31 🖥️ *Practical Demonstration Preparation*
- Prepares for a practical demonstration of molecular dynamics simulation using Gromacs.
01:11:57 💻 *Installing Gromacs on Windows (WSL)*
- Guides on installing Gromacs on Windows using Windows Subsystem for Linux (WSL).
01:16:11 ⚙️ *Preparing Topology File with Gromacs*
- Demonstrates using the `pdb2gmx` module to generate a topology file.
01:21:31 🎉 *Successful Topology File Generation*
- Verifies the successful execution of the `pdb2gmx` command.
01:21:46 📁 *Setting Up Topology File*
- Overview of creating a topology file for molecular dynamics simulation.
01:23:20📦 Solvation *Process (Part 1)*
- Initiating the solvation process by creating a box around the protein.
01:25:39 🚰 *Solvation Process (Part 2)*
- Continuing the solvation process by adding water molecules to the box.
01:27:33 ⚡ *Ionization Process*
- Introduction to the ionization step in molecular dynamics simulation.
01:30:58 🌐 *Preparing TPR File for Energy Minimization*
- Utilizing the "grompp" module to generate the TPR file for energy minimization.
01:37:26 ⚙️ *Energy Minimization*
- Initiating the energy minimization process using the "mdrun" module.
01:39:04 🛠️ *Commercial Services and Q&A Announcement*
- Brief overview of commercial services related to MD simulation.
01:42:14 🔧 *Creating tpr File for NBT Calibrations*
- Demonstrated the process of creating a tpr file for NBT calibrations using Gromacs.
01:44:01 🤔 *Troubleshooting NVT File Selection*
- Identified an issue with the NVT file selection for ligand-protein simulations.
01:44:46 ⚙️ *Initiating Energy Minimization and NBT Preparation*
- Successfully created the tpr file for NBT preparation after resolving the selection issue.
01:45:55 🚀 *Simulation Results and Setup Overview*
- Shared pre-fetched results, including graphs for area, gyration, hydrogen bonds, RMSD, and RMSF.
01:46:52 🖥️ *Overview of Supercomputing Facility and Collaboration*
- Acknowledged the collaboration with a supercomputing facility (RTX 149t) for academic activities.
01:48:31 📂 *Understanding and Modifying MDP Files*
- Explored the content of the MDP (molecular dynamics parameter) file, focusing on the "nsteps" parameter.
01:51:18 📊 *Analyzing RMSD Results Using Excel*
- Shared how to open and analyze RMSD files using Excel for understanding protein stability.
01:54:34 🤝 *Q&A Session: Answering Participant Questions*
- Addressed participant questions regarding missing residues, repairing protein structures, and solvation necessity.
02:00:39 🧪 *Exploring Drug-Protein Interactions*
- Responded to a participant question about assessing drug-protein interaction strength.
02:03:20 🌐 *Exploring Non-Covalent Interactions in Molecular Systems*
- Addressed a question from a participant with a physical chemistry background.
02:04:43 🎨 *Molecular Structure Drawing*
- Drawing three-dimensional molecular structures using software like ChemDraw, Material Studio, or ChemSketch.
02:05:39 🧪 *Force Field Selection and Preparation*
- Decide the appropriate force field based on the molecule's nature.
02:08:50 🔍 *Spectroscopy Properties and Gromacs Modules*
- Install Gromacs modules for specific spectroscopy properties like Raman effect.
02:12:23 ⚙️ *Topology Error Resolution in PDB2GMX*
- Use `-ignh` option to ignore topology errors for one or two amino acid residues.
02:16:07 ⏱️ *Accelerating MD Simulations*
- For faster MD simulations, seek external bioinformatics services.
Made with HARPA AI
thanks dear for your efforts
Your comment is incredible! Thank you so much❤
This webinar is incredibly insightful and valuable. Thank you for sharing your expertise and providing us with a wealth of knowledge.
Our pleasure!
Thank You SIr for this webinar !!!
You are welcome
Nice webinar! The instructions are clear and easy to follow. As a suggestion for future webinars, to avoid background noise, the host could keep his mic muted while the speaker is talking.
Many thanks for your comment. We will take of your suggestion
Thanks for the impactful lecture. My questions are:
1. How do you know if the system's energy is minimized to be bearest?
2. How do you know if the system is completely relaxed?
You can check if the system's energy is minimized by observing the potential energy during the energy minimization process. In GROMACS, after running the energy minimization, you can use the gmx energy tool to analyze the energy minimization log file (.log). Look at the potential energy (Potential) and ensure it reaches a stable minimum value.
A system is considered completely relaxed when it has equilibrated, meaning the properties of the system are stable over time. You can check this by running an equilibration simulation and then analyzing key properties such as temperature, pressure, and density. In GROMACS, you can use the gmx energy tool to extract these properties from the .edr file:
@@bioinfoxpert This is helpful. Thanks
Thank you for wonderful work. Is it necessary that nvt npt and md production time should be same or nvt and npt may be less than final md production
It's not necessary for the NVT, NPT, and MD production times to be the same. Typically, NVT and NPT are equilibration steps, where you allow the system to stabilize at the desired temperature (NVT) and pressure (NPT) before running the production MD simulation. The equilibration time (NVT and NPT) is often shorter than the production MD simulation, which can be run for a longer period to gather sufficient statistical data.
So, you can have shorter NVT and NPT phases, and a longer final MD production run. The key is ensuring that the system is well-equilibrated before starting the production MD.
Sir, please make a dedicated video on accelerated molecular dynamics simulations of protein ligand complex.
Sure I will
Hello sir, I have to do MD Simulation for protein, are that command’s still working for any protein ?
Dear yes, ofcourse do not hesitate to use them
When i use "gmx2pdb -f x.pdb ... NOw, i m getting a warm : "Fatal error: Residue 'UNK' not found in residue topology database." then when I delete the UNK part in pdb file.. there is no warm and error from this code. how to solve this problem while the "gmx2pdb -f ....." is used without not delete the ligands from the pdb file?..thanks
Does anyone have the chrmm file that we need to download from Mackerell website???...the website server is down nowadays..and I need to perform an MD simulation for my research project...Please respond..if anyone have
The ppts is super fantastic. Love it. Please give us some ideas, how can i make such ppts?
Its simple powerpoint tricks
How to repair missing residues
We have already uploaded video for this