2 Day Online Hands-On Workshop on MD Simulation using OpenMM

INTRODUCTION

MD simulation using OpenMM is a highly effective method for studying molecular behavior at the atomic level. OpenMM, an open-source molecular dynamics engine, provides researchers with robust tools to simulate and analyze molecular systems under various physical conditions. From studying proteins and nucleic acids to exploring materials and chemical reactions, OpenMM facilitates a wide range of applications.

Molecular Dynamics (MD) simulation is a computational method where atoms and molecules interact over time, governed by the laws of physics. MD simulation using OpenMM allows researchers to model these interactions in a virtual environment, helping to predict the physical properties, behavior, and stability of molecular systems. OpenMM’s flexibility and extensive support for custom force fields make it an excellent choice for researchers aiming to investigate complex molecular dynamics in real-time.

With OpenMM, users can carry out tasks such as energy minimization, temperature and pressure control, and long-term simulations. Post-MD analysis, including trajectory visualization and property calculations, is also streamlined, allowing researchers to gain insights into molecular interactions, stability, and thermodynamics.

APPLICATIONS OF MD SIMULATION USING OPENMM

• Drug Discovery and Design: OpenMM is widely used in drug discovery to simulate the interaction between drug candidates and their target proteins. Researchers can model how small molecules bind to active sites on proteins, study binding affinities, and optimize drug structures to enhance efficacy and reduce side effects.
• Protein Folding and Dynamics: By simulating how proteins fold into their functional 3D structures, researchers can investigate the causes of misfolding, which is associated with diseases like Alzheimer’s and Parkinson’s, and study potential therapeutic interventions.
• Material Science and Nanotechnology: This includes investigating mechanical properties, thermal stability, and phase transitions of advanced materials, such as polymers, nanomaterials, and semiconductors, under different conditions.
• Membrane Protein Research: OpenMM simulations allow researchers to model these proteins embedded in lipid bilayers, providing insights into their dynamics, interactions with ligands, and the mechanisms of transport across membranes.
• Enzyme Mechanism Elucidation: Researchers can visualize reaction pathways and investigate the impact of mutations on enzyme activity, aiding in enzyme engineering for industrial and therapeutic applications.

DIFFERENT TYPES OF ANALYSIS

• Energy and Stability Analysis: OpenMM allows users to perform energy minimization and analyze energy profiles to understand the stability of molecules, complexes, or materials under different conditions.
• Structural Dynamics: This type of analysis helps in understanding the dynamic behavior of biomolecules like proteins, RNA, or DNA, and how they interact with ligands or other macromolecules.
• Molecular Interaction Analysis: By simulating binding events for studying molecular recognition, drug binding, and complex formation in biological and chemical systems.

TOPICS COVERED

• Introduction to MD Simulation,
• Applications of Python for Running the Process.
• Introduction to OpenMM
• Using OpenMD for Setting-up the Simulation System
• Selecting the forcefield
• Running Equilibration
• Energy Minimization of the simulation system
• Running Main MD Run using OpenMM
• Generating trajectory plots for end-to-end distance and other plots using Matplotlib

TAKEAWAY FROM THE MASTERCLASS

• Introductory Documentation: An introductory theory document to help you better understand the subject will also be provided.
• Trainers Slide Deck: After the completion of the session complete access to the trainers slide deck will also be provided
• Access to Trainers Repo: We will also be providing a complete access to trainers repository so that you can use it as reference later
• 8+ Hours of Live Training: During the course of 3 days we will be have live8+ hourse of training sessions with the participants.
• Guided Hands-On Exercises: Hands-On exercises are a must to better learn any technology and be able to reproduce it later.
• Participation Certificate: A Participations certificate is a must after successfully completing the training as a sign of accomplishment.

EXPECTED OUTCOMES

• Understanding of Molecular Interactions: Researchers can observe the formation and breaking of bonds, non-covalent interactions, and conformational changes in biomolecules or materials, helping to understand mechanisms at the molecular level.
• Prediction of Structural Stability: By simulating molecular dynamics, researchers can predict whether a given molecular structure, such as a protein or a drug-receptor complex, remains stable under physiological or experimental conditions.
• Thermodynamic and Kinetic Properties: OpenMM allows for the calculation of key thermodynamic properties, such as free energy, enthalpy, and entropy, as well as kinetic properties like diffusion coefficients and reaction rates.
• Validation of Experimental Data: By comparing simulated structures and dynamics to experimental data, researchers can confirm hypotheses about molecular behavior or propose new explanations for observed phenomena.

TERMS & CONDITIONS

• All fee paid is not refundable so please read all the terms & conditions before making any payments. If you still have any doubts please contact us and confirm and then only make the payment.
• Participants need to bring their registration tickets along with a valid Institutional ID, then only they will be allowed to attend the session. Please reach out to our team in case of any exceptions.
• Please fill all your details in the form correctly as those details will be used in your certificate as well.
• Participants need to bring their own computer (laptop) system for the program.
• The software tools and other required software tools will be provided from our side for the purpose of this program.
• Participants need to reach the venue and report 30 minutes prior to the start of the sessions.
• Participants need to wear masks all the time inside the premises and abide by the other rules at the premises.
• Particpants need to attend all the sessions in order to be eligible for getting the certificate.
• Welcome email will be sent to all the participants with all the details related to the program. Please check your Inbox/Spam folder for the email.
• All the details of the software installations and how to prepare your system for the Program will be shared with all the participants in the Welcome Email itself.