Advanced Molecular Dynamics Simulation:

A Summer School 2021

Starts: July 5, 2021
Ends: July 16, 2021

ZOOM Venue

Introduction

Welcome to the Advanced Molecular Dynamics workshop where you can learn both the concepts and application of molecular dynamics simulation from the top experts of the field. Scope of the workshop captures molecular dynamics simulations, enhanced sampling methods and QMMM simulations. The workshop is jointly organized by the Department of Chemistry, IISER Pune, Department of Physics, and the Green Club of Thoughts, Kathmandu University. We are offering specialized classes, hands on tutorial sessions and guest lectures from experts of the field. Checkout our guest speakers section.

Whether you are a graduate student, young researcher or early career faculty, you can benefit from our two weeks workshop. In the first week, you can learn basics of LINUX OS, software installation, virtual machine, HPC architecture, data visualization and other necessary trainings such that you are ready for advanced MD school. The second week is focused on advanced MD simulations, post-processing and several analysis methods. The morning session of the second week will consist of lectures on the basic principles and methodologies followed by a special lecture covering experimental and theoretical aspects of MD simulations. The afternoon sessions will consist of hands-on tutorial sessions where the participants will do simple and advanced calculations using the GROMACS and CHARMM. Each day will conclude with Guest lectures delivered by field experts which will further enrich your understanding about scope of MD simulations. We are also offering access to HPC facilities (both CPU and GPU) for following month to familiarize and train yourselves with the concepts taught in the school.

Topics Covered

Week 1

  • Time: [1:45pm - 5:00pm]
  • Teaching Assistants: Mr. Sai Raj Ali & Dr. Subrahmanyam Sappati. & Dr. C.S. Praveen

  • Time: [1:45pm - 5:00pm]
  • Dr. Subrahmanyam Sappati. & Mr. Shirshak & Dr. Nandhakumar V.

  • Time: [1:45pm - 5:00pm]
  • Teaching Assistants: Dr. Niharika Joshi & Dr. Subrahmanyam Sappati.

  • Time: [1:45pm - 5:00pm]
  • Teaching Assistants: Dr. Reman Kumar & Dr. Subrahmanyam Sappati

  • Time: [9:00am - 10:30am]
  • Topics: FFParam and QMMM input
  • Teaching Assistants: Dr. Anmol kumar & Dr. Subrahmanyam Sappati
  • Time: [1:45pm - 5:00pm]
  • Teaching Assistants:Ms. K. Kavya & Dr. Rajendra Adhikari & Mr. Sarun Jonchhe

Week 2

  • Class
    • Intro To MD
    • Time: [9:00am - 10:30am]
    • Prof. Arnab Mukherjee
  • Specialized Class
    • MD Simulation in Nepal Yesterday, Today and Tomorrow.
    • Time: [11:00am - 12:30pm]
    • Prof. Narayan Adhikari
  • Tutorial
    • Water Simulations SPC/E , TIP3P, TIP4P
    • Water and Calcium + Amides
    • Time: [2:00pm - 5:00pm]
    • Dr. Bappa Ghosh and Dr. Reman Kumar Singh

  • Class
    • Enhanced Sampling Methods
    • Time: [9:00am - 10:30am]
    • Prof. Arnab Mukherjee
  • Specialized Topic
    • Force Field Development For Ionic Liquids
    • Time: [11:00am - 12:30pm]
    • Prof. Balasubramanian Sundaram
  • Tutorial
    • Water and Calcium + Amides
    • Protien Drug
    • Time: [2:00pm - 5:00pm]
    • Dr. Rakesh Pant and Dr. Reman Kumar Singh
  • Guest Lecture
    • SILCS: A multifaceted tool for drug design using GCMC/MD approach
    • Time: [6:30pm - 7:30pm]
    • Prof. Alexander D. MacKerell Jr.

  • Class
    • Thermostats And Algorithm
    • Time: [9:00am - 10:30am]
    • Prof. Sajeev Chacko
  • Specialized Topic
    • A Molecular Thermodynamic View of Biomolecular Recognition and Signalling
    • Time: [11:00am - 12:30pm]
    • Prof. Suman Chakrabarty
  • Tutorial
    • Umbrella Sampling and Well-Tempered Metadynamics
    • Time: [2:00pm - 5:00pm]
    • Dr. Reman Kumar Singh
  • Guest Lecture
    • Molecular Tailoring Approach: ab initio Treatment of Large Molecular Systems
    • Time: [6:00pm - 7:00pm]
    • Prof. Shridhar R. Gadre

  • Class
    • QM/MM Energy Calculations (input description)
    • Time: [9:00am - 10:30am]
    • Dr. Anmol Kumar
  • Specialized Topic
    • QMMM Theory (Title to be updated)
    • Time: [11:00am - 12:30pm]
    • Prof. Prasenjit Ghosh
  • Tutorial
    • QM/MM Setup (via CHARMM)
    • Time: [2:00pm - 5:00pm]
    • Dr. Anmol kumar
  • Guest Lecture
    • Identifying valuable diversity in Cannabis, using genomic sequence data
    • Time: [6:00pm - 7:00pm]
    • Prof. Nolan Coburn Kane

  • Class
    • QM/MM Simulations
    • Time: [9:00am - 10:30am]
    • Dr. Anmol Kumar
  • Specialized Topic
    • (To be decided)
    • Time: [11:00am - 12:30pm]
    • Prof. Partha Hazra
  • Tutorial
    • QM/MM Simulation
    • Time: [2:00pm - 5:00pm]
    • Dr. Anmol kumar
  • Concluding Remarks

Guest Speakers

Teaching Assistants

  • Dr. Subrahmanyam Sappati
    • Raman Research Institute
  • Dr. Niharika Joshi
    • National Chemistry Lab, Pune
  • Dr. Reman Kumar Singh
    • IIT Bombay
  • Dr. Anmol Kumar
    • University of Maryland, USA
  • Mr. Rajendra Koirala
    • Central Department of Physics, Tribhuvan University
  • Dr. Bappa Ghosh
    • IISER-TVM
  • Dr. C.S. Praveen
    • CUSAT
  • Dr. Rajendra Adhikari
    • Kathmandu University
  • Dr. Rakesh Pant
    • IIT Bombay
  • Mr. Mohammed G
    • University of Mumbai
  • Mr. Sai Raj Ali
    • Jamia Millia Islamia University, New Delhi
  • Mr. Sarun Jonchhe
    • Kathmandu University
  • Mrs. K. Kavya
    • IVRI-Bangalore, India
  • Dr. Sathish Dasari
    • IIT Hyderabad
  • Dr. Nandhakumar V.
    • ICTP, Italy

How To Register

  1. Registration Fee:

  2. For the faculty : NPR 4999 (INR 5000)
  3. For Postdocs : NPR 3999 (INR 3500)
  4. For Students : NPR 2999 (INR 2000)








  5. PAYMENT CLOSED

Contact Details

  1. Dr. Rajendra Adhikari
  2. Dr. Subrahmanyam Sappati
  3. Dr. Reman Kumar Singh
  4. Mr. Ashim Joshi
Closed

Registration CLosed

Organizers

Department of Physics, Kathmandu University
Department of Chemistry, IISER Pune
Green Club of Thoughts Kathmandu University

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