Biology Events

Online Workshop on GROMACS

Biology Events, Chemistry Events, Upcoming Events /

Training Program on GROMACS Molecular Dynamics MD Menu All Events Upcoming Events Past Events Testimonials Request For Collaboration Two-Week Online Workshop on GROMACS Introduction to Molecular Dynamics Register Now Date 08 – 19 Sept 2025 Time 07.30 pm IST About the Workshop This two-week online hands-on training on GROMACS is designed to provide participants with comprehensive knowledge and practical experience in molecular dynamics (MD) simulations. The workshop covers a wide range of topics—from fundamental concepts of MD and high-performance computing (HPC) to advanced simulations involving protein-ligand, membrane-protein, metal complexes, and nanomaterial interactions. Participants will gain hands-on experience using GROMACS tools, simulation setup, data analysis, and visualization techniques.   The program also introduces web-based resources like CHARMM-GUI and covers workflows for real-world biomolecular systems. This workshop is ideal for students, researchers, and professionals from chemistry, biology, physics, and computational sciences seeking to enhance their skills in molecular simulation. Target Audience Students, Researchers and faculty members of Biology, Chemistry, Physics and material science  Key Topics: Introduction to MD Simulations Installation & Workflow Analysis and Visualization Protein-Ligand Simulations Protein-Metal Complex/Nanomaterial Simulations Features Step-by-step Simulation Workflows Assignments and Practical Exercises Recordings will be available. eCertificate will be provided Optional HPC Access Participants can avail remote High-Performance Computing (HPC) access for 1 month to run their simulations efficiently with a nominal fee of Rs. 2500. Recordings & Certificate Recordings of live sessions will be available for future reference. Participants will receive an e-certificate of completion.  Course Plan Please download the course plan from the link provided below. Download Course Plan  Download Flyer  Schedule Two-Week Workshop on GROMACS Day & Time Session Topics Link Day 1, 07.30 pm Introduction to Molecular Dynamics (MD) Introduction to MD simulations: Numerical recipe for running MD simulations, basic algorithm, software used for MD simulations Aim and information obtained from MD simulations Introduction to basics of high-performance computing (HPC) Introduction to the ‘inSilicoLab’ HPC system and its function, running jobs, allocation of resources, file sharing protocols, installed software packages, location of the software executables Day 2, 07.00 pm Introduction to Gromacs Introduction to Gromacs MD simulation package How to install Gromacs on Ubuntu OS, (for Windows OS, installing Ubuntu on a virtual machine and installing gromacs there), how to install gromacs for cpu only and gpu machines Workflow for running MD simulations in gromacs Introduction to files, file formats, units, constants in gromacs Basics of protein structure (primary, secondary & tertiary), structure file formats (gro file, pdb file), RCSB data bank, uniport, how to download pdb file Day 3, 07.30 pm Calculations using Gromacs Setting up a protein in water simulation (ubiquitin, lysozyme protein in water) in gromacs Step-by-step guide and hands-on workflow of using gromacs to setup protein in water simulation Running MD simulation on HPC server from command prompt and job script Day 4, 07.30 pm Analysis of the MD simulation data Analysis of the MD simulation data using gromacs tools Visualization of simulation trajectories using VMD Assignment for ubiquitin simulation Day 5, 07.30 pm Accessing GUI-based software tools on the server Introduction to web-based tools (e.g. Charmm-gui) for input preparation Preparing lipid-bilayer or membranes using charmm-gui Introduction to MD simulation setup of membrane-protein in water Preparing peptide-membrane simulation system Day 6, 07.30 pm Introduction to protein-ligand MD simulations in Gromacs Obtaining protein and Ligand parameters Running protein-ligand MD simulations Introduction to free-energy calculations Day 7, 07.30 pm Protein-Metal Complex MD simulations in Gromacs Obtaining protein and Ligand parameters Running protein-ligand MD simulations Day 8, 07.30 pm Protein-Nanomaterials MD simulations in Gromacs Obtaining protein and Ligand parameters Running protein-ligand MD simulations Day 9, 07.30 pm Analysis of the results Obtaining protein and Ligand parameters Running protein-ligand MD simulations Day 10, 07.30 pm Doubt-Clearing Session Doubt-Clearing Session Resource Persons Github Linkedin Facebook Google-plus Dr. SM Abdul Fayaz Associate Professor Department of Biotechnology Manipal Institute of Technology (MIT) Manipal Academy of Higher Education (MAHE), Manipal Github Linkedin Facebook Google-plus Dr. Bibhab Majumdar Assistant Professor Department of Chemistry School of Advanced Sciences, VIT-AP University, Amaravati, Andhra Pradesh Github Linkedin Facebook Google-plus Github Linkedin Facebook Google-plus Registration Registration Fee Rs. 3000 Rs. 2500 (for HPC) Register Now Registration Fee For Indian Participants: Rs. 3000Foreign Participants: USD 50 SIAS Research Forum MembersStudent Member: Rs. 2700Faculty Member: Rs. 2400 HPC Charge: Rs. 2500 (optional) Feedback from the participants We will update this part after the compltion of the workshop! 

Online Workshop on GROMACS Read More »

One-Week Workshop on OriginPro

Biology Events, Chemistry Events, Physics Events, Previous Events /

Training Programs OriginPro for beginner! Graph Drawing! Data Analysis! Graph Fitting! Menu All Events Upcoming Events Past Events Testimonials Request For Collaboration 10-Day Online Hands-on Training on OriginPro Graphing & Data Analysis Register Now Date 11 – 22 June 2025 Time 07.30 pm IST About the Workshop This program is designed with practical knowledge and skills in using ORIGIN – a powerful data analysis and graphing software widely used in scientific research. Participants will explore Origin’s interface, graphing capabilities, data analysis tools, peak analysis, curve fitting, and various exporting and publishing features. Whether you are a beginner or looking to enhance your proficiency, this program offers valuable insights into efficient data visualization and analysis using Origin. Target Audience UG, PG students, researchers, and faculty members of biology, chemistry, physics and Engineering  Tools to be used Origin Computer Configuration: Windows Recording for Future Referenece All live sessions will be recorded and made available to participants, ensuring they have access to the content for future reference.  Topics Introduction to Origin Interface Graphing Data Analysis Peak Analysis Advanced Curve Fitting Save and Export Data Course Completion Certificate​ At the end of the workshop, participants will receive an e-certificate of completion. Course Plan Please download the course plan and  Brochure from the links provided below. Download Schedule Brochure  Schedule 10-Day Online Hands-on Training on OriginPro Day & Time Session Topics Link Day 1, 07.30 pm Introduction to Origin Interface Installation and introduction of Interface Origin File Types Import Data Workbooks, Worksheets and Columns Matrix Books, Matrix Sheets and Matrix Objects Day 2, 07.30 pm Graphing Drag and Drop Plotting Plot XY Data, XYY Data, Multiple Y Axis Box & Violin Plots XYZ Contour Plots XYZ 3D Surface and Scatter Graph Maker and Duplicate Easily change fonts on a Graph Merge Graph, Arrange Layers, Managing Layers Display the Opposite Axis with Nonlinear Formula Copy/Paste Plots and Layers Publishing Day 3, 07.30 pm Data Analysis Preserving Data Connector Data Recalculation Mode and Lock Icons Day 4, 07.30 pm Peak Analysis Peak Finding Fitting Multiple Datasets Lorentzian and Gaussian Fitting Sequential Fit App Bounds and Constraints Implicit and Surface Fitting Peak Convolution & Peak Integration 3D Peak Batch Peak Analysis Day 5, 07.30 pm Advanced Curve Fitting Simple Fit Tools and Process (Step by Step Creating Fitting Function) Expression-Based functions Fitting Function Builder More Complex Functions Function with Integration – Integration Fitting Function by Expression in FFB Day 6, 07.30 pm Save and Export Data Send Graph to PPTX Save a different format to access the data and graph directly Day 7, 07.30 pm Apps in Origin Chromacity diagram, Batch Plotting, peak convolution, Maps Online etc. Worksheet Cells, Smiles Inserting HTML & Markdown Report Add References and Linear Fit Lines to a Plot Day 8, 10.00 am Plot Aesthetics Plotting statistical data Masking bad data Interpolation of columns Beautification of Plots Day 9, 07.30 pm Scientific data analysis Data analysis of Photoluminescence & Raman spectroscopy Peak, FWHM, Integrated area analysis Day 10, 07.30 pm Advanced curve fitting Advanced curve fitting with experimental dat Statistics of experimental data. Interpolation data Resource Person Github Linkedin Facebook Google-plus Dr. Pradeep Reddy Assistant Professor, Vel Tech Rangarajan Dr. Sagunthala R and D Institute of Science and Technology, Chennai Github Linkedin Facebook Google-plus Dr. Akant Sharma Postdoctoral Researcher, Sapienza University of Rome, Italy Github Linkedin Facebook Google-plus Github Linkedin Facebook Google-plus Registration Registration Fee Rs. 2000 Register Now Registration Fee For Indian Participants: Rs. 2000Foriegn Participants: USD. 40 SIAS Research Forum MembersStudent Member: Rs. 1800Faculty Member: Rs. 1600 Feedback from the participants We will update this part after the compltion of the workshop! 

One-Week Workshop on OriginPro Read More »

Nine-Day Workshop on Molecular Docking

Biology Events, Chemistry Events, Physics Events, Previous Events /

ChemDraw Training Full Potential! Best Dreams! Sufficient impossible him may ten insensible put continuing. Oppose exeter income simple  twenty. Menu All Events Biology Chemistry Physics Data Science Material Science Testimonials Request For Collaboration One-Week Online Workshop on ChemDraw About The Event Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut commodo consequat duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur excepteur sint occaecat. 14 – 21 June 7.30 pm IST Course Plan Register Now Event Schedule Day 1 14-June, 7.30 pm IST Introduction to ChemDraw How to draw Organic Molecules Dr. Rajkumar G Assistant Professor Day 2 14-June, 7.30 pm IST Advanced Techniques Drawing Chemical Reactions Dr. Rajkumar G Assistant Professor Day 3 14-June, 7.30 pm IST Analysis using ChemDraw Properties prediction Dr. Rajkumar G Assistant Professor Day 4 14-June, 7.30 pm IST Chem3D Drawing 3D molecules Mr. Jibin S Research Scholar Day 5 14-June, 7.30 pm IST Chem3D: Calculations MM calculations using Chem3D Mr. Jibin S Research Scholar Day 6 14-June, 7.30 pm IST ChemDraw for Excel MM calculations using Chem3D Mr. Bobby Solanki Senior Technical Consultant, SCUBE Day 6 14-June, 7.30 pm IST Doubt-Clearing Session Assignments Discussion Dr. Sabeel M Basheer Assistant Professor Speakers Dr. Rajkumar G Assistant Professor Dr. Sabeel M Basheer Assistant Professor Mr. Bobby Solanki Art Director – Globex Mr. Jibin S Research Scholar Workshop Features Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut commodo consequat duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur excepteur sint occaecat. Cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. Sed ut perspiciatis unde omnis iste natus error sit voluptatem accusantium doloremque laudantium, totam rem aperiam, eaque ipsa quae ab illo inventore veritatis. Registration Fee Indian Participants: Rs. 1500  Foriegn Participants: USD. 40  SIAS Research Form Student Member: Rs. 1350 SIAS Research Forum Faculty Member: Rs. 1200 Register Now Feedback from particiapnts! “Attending this ChemDraw workshop is a great opportunity to enhance my skills in molecular drawing and chemical structure visualization. The workshop typically covered a range of topics, from basic functionalities to advanced techniques like reaction mapping and 3D structure generation. I learned a lot from this workshop. Hope you will continue conducting such workshops in future also..thanks to the organising team of this workshop.” Dr.Babita Chaudhary Assistant Professor, Vardhaman College, Bijnor “The resource persons explained ChemDraw in a clear and understandable manner, which was very helpful for a beginner like me.” Manju P K Assistant Professor, Govt Polytechnic College, Kaduthuruthy “When I first saw the fee of the workshop 1500 rupees for Chemdraw a bit expensive i felt but once sessions started and knowing the things we did not know about the chemdraw it was completely worth finally its wondeerful workshop I am happy that I did not miss it.” Mokhamatam Sudheer Andhra University

Nine-Day Workshop on Molecular Docking Read More »

One-Week Workshop on Molecular Dynamics

Biology Events, Chemistry Events, Previous Events /

Training Programs Molecular Dynamics for beginner! MD Simulations using GROMACS! GROMACS! Menu All Events Upcoming Events Past Events Testimonials Request For Collaboration Workshop on Molecular Dynamics Simulations One-Week Online Workshop on Molecular Dynamic Simulations GROMACS or NAMD Register Now Date 05 -12 Aug 2024 Time 07.30 pm IST About the Workshop Join us for an intensive one-week online workshop on Molecular Dynamics (MD) Simulation using GROMACS or NAMD. This workshop is designed to provide a comprehensive understanding of the principles and practical applications of MD simulations in biomolecular research. Participants will learn how to set up and perform simulations, analyze the results, and gain insights into the dynamic behavior of molecular systems. The workshop will utilize open-source tools such as GROMACS or NAMD, VMD, and other essential software, making it accessible for researchers and students alike. Target Audience Students, Researchers and faculty members of biology, chemistry, physics who are interested in learning about molecular dynamics simulations. Tools to be used NAMD/GROMACS, VMD, and others (All open-source Tools) Computer Configuration: Linux (preferred), macOS, or Windows Recording for Future Referenece All live sessions will be recorded and made available to participants, ensuring they have access to the content for future reference and continued learning.  Topics Installation of software Simulation of Protein (receptor) Structure and of Receptor-Ligand Complex and Analysis of Results Course Completion Certificate​ At the end of the workshop, participants will receive an e-certificate of completion, recognizing their effort and newfound skills in GROMACS and Molecular Dynamics. Course Plan Please download the course plan and  Brochure from the links provided below. Download Now  Brochure  Schedule One-Weeek Workshop on Molecular Dynamics Simulation Day & Time Session Topics Link Day 1, 07.30 pm Theoretical principles related to MD Simulation Introduction to the fundamental concepts of molecular dynamics Force fields, integration methods, and the importance of time steps in simulations Installation of GROMACS or NAMD Day 2, 07.30 pm System Setup for Simulation Detailed walkthrough of preparing a system for MD simulation Selection and preparation of biomolecules, solvation, ion addition, and energy minimization Troubleshooting installation issues Day 3, 07.30 pm Simulation of Protein (receptor) structure Simulating protein structures Equilibrate the system and run production MD simulations Day 4, 07.30 pm Simulation of Receptor-Ligand complex Explore the dynamics of receptor-ligand interactions Docking and binding site analysis Conformational changes upon ligand binding Day 5, 07.30 pm Analysis of Results Methods and tools for analyzing MD simulation results Trajectory analysis, calculation of RMSD, RMSF Hydrogen bonds, and secondary structure analysis Visualization tools like VMD to interpret and present the findings effectively Day 6, 07.30 pm Assignment/ Q&A Discussion Doubt-Clearing Session Resource Person Github Linkedin Facebook Google-plus Dr. Shaik Mohammad Abdul Fayaz Assistant Professor Department of Biotechnology Manipal Institute of Technology (MIT) Manipal Academy of Higher Education (MAHE) Manipal, Karnataka, India Github Linkedin Facebook Google-plus Github Linkedin Facebook Google-plus Registration Registration Fee Rs. 2500 Register Now Registration Fee For Indian Participants: Rs. 2500Foriegn Participants: USD. 40 SIAS Research Forum MembersStudent Member: Rs. 2250Faculty Member: Rs. 2000 Feedback from the participants We will update this part after the compltion of the workshop! 

One-Week Workshop on Molecular Dynamics Read More »