Advanced Molecular Dynamics Simulation:

A Winter Workshop 2021

50years
Starts: Sep 6, 2021
Ends: Sep 17, 2021
ZOOM Venue
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Introduction

This workshop aims at introducing graduate students, young researchers and early career faculties primarily from Asian countries (but also from elsewhere), to the basic to advanced concepts of MD simulations and an introduction session to the state-of-the-art Machine Learning Techniques. This workshop is divided into two weeks. The first week of the workshop is mainly focused on the basics of MD, a variety of computational software and uses of HPC facilities as well as a special session on 3D rendering via "Blender" software, and other necessary training to handle the advanced lectures to follow on the second week of the workshop. The latter is focused on MD simulations with the interpretation of results and introduction to some post-processing techniques.

The morning sessions of the workshop will consist of lectures on the basic principles and methodologies followed by a special lecture or research talks (covering experimental and theoretical aspects) showing their applications. The afternoon sessions will consist of hands-on tutorials where the participants will do simple and advanced calculations using the GROningen MAchine for Chemical Simulations (GROMACS), and an introduction session to Machine Learning techniques. Further, the school provides access to HPC facilities (both CPU and GPU architecture) for a month to familiarise and train themselves with the concepts taught in the workshop.

Topics Covered

  Week 1

  • Morning Session
    • Topic: Introduction to ZOOM/Slack/VM platform.
    • Time: [9:00 - 12:00]
    • Resource Person:
      • Mr. Sai Raj Ali (JMI, New Delhi),
      • Dr. Praveen C. S. (CUSAT, Kerala),
      • Dr. Rajendra Adhikari (KU, Nepal)
  • Afternoon Session:
    • Topic: Introduction to LINUX OS and Vi/Emacs.
    • Time: [2:00 - 4:00]
    • Resource Person:
      • Dr. Satish Dasari (IIT-H)

  • Morning Session
    • Topic: Bash/Csh/Shell scriptwriting and Discussion on visualisers VMD/CHIMERA.
    • Time: [09:00 - 12:00]
    • Resource Person:
      • Dr. Niharika Joshi (NCL)
      • Dr. Nandhakumar V (ICTP)
      • Dr. Sathish Dasari (IIT-H)
      • Dr. Reman Kumar S (IIT B)
  • Afternoon Session:
    • Topic: Python script.
    • Time: [2:00 - 4:00]
    • Resource Person:
      • Dr. Asish M. Desai (PCC Goa)
      • Mr. Castor Godinho (PCC Goa)
      • Mr. Wendham Gray (PCC Goa)

  • Morning Session
    • Topic: Plotting Softwares & HPC access
    • Time: [09:00 - 12:00]
    • Resource Person:
      • Dr. Niharika Joshi (NCL)
      • Mr. Sai Raj Ali (JMI, New Delhi)
  • Afternoon Session:
    • Topic: A case study of SARS-Cov-2 and inhibitors Introduction on ADFR tools
    • Time: [2:00 - 4:00]
    • Resource Person:
      • Mrs. K. Kavya (IVRI-Bangalore)
      • Ms. Sandra Jose (IIT-G)
      • Mr. Sarun Jonchhe (KU, Nepal)

  • Morning Session
    • Topic: Hands-on Auto-docking (HPC).
    • Time: [09:00 - 12:00]
    • Resource Person:
      • Mr. Sarun Jonchhe (KU, Nepal)
      • Dr. Rajendra A (KU, Nepal)
      • Ms. Aishwarya Dharan (CUPB)
      • Ms. Sandra Jose (IIT-G)
  • Afternoon Session
    • Topic: 3D rendering software.
    • Time: [02:00 - 04:00]
    • Resource Person:
      • Mr. Rafeeque M (SciDart)

  • Discussion/ Assistance on Slack

    • Discussion/ Assistance on Slack
    • Evening Session:
      • Topic: Introduction to MD
      • Time: [6:00 - 7:30]
      • Resource Person:
        • Dr. Anmol Kumar (University of Maryland Baltimore, USA)

Week 2

  • Lecture-1
    • Topic: Quantitative structure-activity relationship (Title to be updated).
    • Time: [9:00 - 10:15]
    • Resource Person:
      • Prof. Dr. Mukesh Doble (IIT Madras)
  • Case-Study-1:
    • Topic: In silico observations leading to in vitro experiments : a case study
      using molecular docking and molecular dynamics. (Tentative)
    • Time: [11:00 - 12:15]
    • Resource Person:
      • Dr. K N Naresh (Asst. Professor, Biosciences,SSSIHL)
  • Hands-On Session-1:
    • Topic: Quantitative structure-activity relationship (QSAR) Hands-On.
    • Time: [2:00 - 4:00]
    • Resource Person:
      • Prof. Dr. Mukesh Doble (IIT Madras)
  • Hands-On Session-2:
    • Topic: Hands-on MD [Basics of MD/Forcefield/..]
    • Time: [4:10 - 5:00]
    • Resource Person:
      • Dr. Reman Kumar S (IIT Bombay)
      • Dr. Satish Dasari (IIT Hyderabad)
      • Dr. Subrahmanyam S (RRI Bangalore)
      • Sathya Sai Kiran

  • Lecture-1
    • Topic: MD Simulation in Nepal Yesterday, Today and Tomorrow (Title to be updated).
    • Time: [9:00 - 10:15]
    • Resource Person:
      • Prof. Narayanan Adhikari (KU, Nepal)
  • Case-Study-1:
    • Topic: Enhanced sampling methods
    • Time: [11:10 - 12:15]
    • Resource Person:
      • Dr. Santosh Mogurampelly, (Associate professor, IIT Jodhpur)
  • Hands-On Session:
    • Topic: Hands-on MD [Protein]
    • Time: [2:00 - 4:00]
    • Resource Person:
      • Dr. Reman Kumar S (IIT Bombay)
      • Dr. Satish Dasari (IIT Hyderabad)
      • Dr. Subrahmanyam S (RRI Bangalore)
  • Lecture-2:
    • Topic: Identifying valuable diversity in Cannabis, using genomic sequence data
    • Time: [6:00 - 7:15]
    • Resource Person:
      • Prof. Nolan Coburn Kane,(University of Colorado, Boulder, USA)

  • Hands-On Session-1:
    • Topic: Hands-on MD [Enhanced Sampling].
    • Time: [9:00 - 10:15]
    • Resource Person:
      • Dr. Reman Kumar S (IIT Bombay)
      • Dr. Satish Dasari (IIT Hyderabad)
      • Dr. Subrahmanyam S (RRI Bangalore)
  • Hands-On Session-2:
    • Topic: Hands-on MD [Enhanced Sampling].
    • Time: [11:00 - 12:15]
    • Resource Person:
      • Dr. Reman Kumar S (IIT Bombay)
      • Dr. Satish Dasari (IIT Hyderabad)
      • Dr. Subrahmanyam S (RRI Bangalore)
  • Lecture-1:
    • Topic: AIMD (Title to be updated)
    • Time: [2:00 - 4:00]
    • Resource Person:
      • Prof. Sandro Scandlo (ICTP-Trieste, Italy)
  • Lecture-2:
    • Topic: AIMD Tutorial.
    • Time: [5:00 - 6:45]
    • Resource Person:
      • Dr. Riccardo Bertossa (SISSA, Italy).

    • Topic: Python Script
    • Time: [9:00 - 10:00]
    • Resource Person:
      • Dr. Niharika Joshi (NCL Pune)
    • Topic: Data Structure
    • Time: [10:00 - 12:00]
    • Resource Person:
      • Dr. Niharika Joshi (NCL Pune)
      • Castor
      • Wendham
  • Afternoon Session
    • Topic: Recap of MD Tutorial
    • Time: [2:00 - 4:00]
    • Resource Person:
      • Dr. Reman Kumar S (IIT Bombay)
      • Dr. Satish Dasari (IIT Hyderabad)
      • Dr. Subrahmanyam S (RRI Bangalore)

  • Hands-On
    • Topic: Case Study-1 (Title to be updated).
    • Time: [9:00 - 10:15]
    • Resource Person:
      • Dr. Indra Dev Sahu (Campbellsville University, USA)
  • Hands-On:
    • Topic: Dendrimer Interactions with Pore Forming Toxins (PFTs) (Tentative)
    • Time: [11:00 - 12:15]
    • Resource Person:
      • Dr. Subbarao Kanchi, SSSIHL, India.
  • Lecture:
    • Topic: Deadline of the project 1 and 2.
    • Time: [2:00 - 3:00]
    • Resource Person:
      • Dr. Subrahmanyam S (RRI Bangalore)
      • Mr. Rafeeque M (SciDart)

  • Lecture:
    • Topic: Introduction to Machine Learning.
    • Time: [06:00 - 07:30]
    • Resource Person:
      • Dr. Anmol Kumar (University of Maryland Baltimore, USA)

Guest Speakers

Teaching Assistants

  • Dr. Subrahmanyam Sappati
    • Raman Research Institute
  • Dr. Praveen C. S.
  •        CUSAT-Kerala
  • Dr. Reman Kumar Singh
    • IIT Bombay
  • Dr. Anmol Kumar
    • University of Maryland, USA
  • Dr. Rajendra Adhikari
    • Kathmandu University
  • Dr. Niharika Joshi
    • National Chemistry Lab, Pune
  • Dr. Sathish Dasari
    • IIT Hyderabad
  • Dr. Mohammed Ghadiyali
    • University of Mumbai
  • Dr. Nandhakumar V
    • ICTP, Italy
  • Dr. Asish M Desai
    • Parvatibai Chowgule College Goa
  • Dr. Suryabrahmam Buti
    • Raman Research Institute

  • Mr. Sai Raj Ali
    • Jamia Millia Islamia University, New Delhi
  • Mr. Sarun Jonchhe
    • Kathmandu University
  • Mr. Shirshak
    • Kathmandu University
  • Mrs. K. Kavya
    • IVRI-Bangalore, India
  • Ms. Sandra Jose
    • IITG
  • Ms. Aishwarya Dharan
    • CUPB
  • Mr. Sumanth 
    •  Raman Research Institute
  • Mr. Castor Godinho 
    •  Parvatibai Chowgule College Goa
  • Mr. Wendham Gray 
    •  Parvatibai Chowgule College Goa
  • Mr. Bratin Kumar Das
    •  NITK, Surathkal


    Click Here To Register

    1. Registration Fee:

    2. For the faculty : INR 5000 (NPR 8000)
    3. For Postdocs : INR 3500 (NPR 5600)
    4. For Students : INR 2000 (NPR 3200)
    Registration open

    Click on above links for the payment

    Contact Details

    1. Dr. Rajendra Adhikari
    2. Dr. Praveen C. S.
    3. Mr. Rafeeque Mavoor
    4. Mr. Ashim Joshi

    Organizers


    International School of Photonics, Cochin University of Science And Technology (CUSAT), India
    Department of Physics, Kathmandu University
        Green Club of Thoughts Kathmandu University


         
            Scidart Academy

    Sponsors

    NREN
    Subishu