GROMACS, VMD & NAMD 8 Day Certificate Online Training | Event in NA | Townscript
GROMACS, VMD & NAMD 8 Day Certificate Online Training | Event in NA | Townscript

GROMACS, VMD & NAMD 8 Day Certificate Online Training

Sep 23 - 30 | 06:00 AM (IST)
Online Event

Event Information

BDG LifeSciences (OPC) Pvt. Ltd. India is a Bioinformatics company with expertise in conducting Workshops, Training, Novel Research Projects & Online Courses in technologies of Bioinformatics and is in business since 2010. Being proficient in Drug Discovery & Designing, MD Simulations, NGS Data Analysis, and Gene & Genome Editing by CRISPR/Cas9 to date, we have successfully trained hundreds of participants who were not only students but scientists, faculties, professors, company executives, etc across the world.
As we believe in a different way of learning which is HANDS-ON PRACTICAL SESSIONS our workshops are unique because participants perform on their own computer/laptop on software/servers, so it is a 100 % practical application of technology which is the main reason of BEING A LEADER in the sector for the last 10 years. To view the pictures of our previous events click here-1 and click here-2. To view, the listing of upcoming events kindly click here and our previous workshops can be viewed here. To view the video feedback of our previous events kindly visit our YouTube Channel

To cater to the need of a huge demand for learning MD Simulations on Linux by GROMACS and on Windows by NAMD we have launched an 8-day Certificate Training Program in Practical approach in Molecular Modeling Dynamics & Simulations | Insights of Computational Biophysics in which every day 2-hour interactive training session on Google Meet/Zoom will be conducted to give the user a unique learning experience. Video recording of each session will be provided at the end of the session to give the user a unique learning experience. On successful completion of the course participation certificate will be awarded. After lectures and discussions, participants will learn how to model a biological molecule such as a particular protein, solvate the protein, run minimization, equilibration, and protein simulation, and analyze the simulations.

TOPICS
THEORY OF MD SIMULATIONS 
STEPS OF MD SIMULATIONS

WINDOWS OS
Using NAMD 2.9 Simulation is performed.
VMD is used to prepare required input files
1. Preparation of input files
         1.PDB files
          2.PSF files
          3.CHARMM force field parameters files
          4. Configuration files
2. Solvating target
3. Simulation
        1.Simulation with periodic boundary conditions
        2.Simulation with nonperiodic boundary conditions
        3.Simulation in GBIS.
3. Methodology for the analysis of VMD and NAMD results.
4. Analysis of NAMD Plots with all the parameters
5. RMSD calculation
6. Energy calculation.
7. Simulation Analysis
8. Reading extract files at each time step
9. Interpretation of NAMD Plots and visualization in 3D

PRACTICAL APPLICATION
1. VMD tk console windows
2. NAMD 2.command prompt
 Creation of output files
.Coor
.xsc
.vel
.log
3. Plotting NAMD Plots in VMD window.
4. Interpretation of NAMD Plots

LINUX OS
INSTALLATION OF GROMACS ON LINUX USING LINUX COMMANDS
create initial state
1) Generation of topology for protein
2) add box and solvation of system
3) add ions to the solvated system
Energy minimization OF SYSTEM
Equilibration of system
MD production run
Analysis by xmgrace and VMD

TARGET AUDIENCE
Student: Bachelor, Masters, PhD, MBBS, MD students as well as Faculty and Professors from Microbiology, Biochemistry, Biotechnology, Immunology, Medicine, Pharmacy, Pharmaceutical Chemistry, Biomedical Technology, Genetics, Bioinformatics, Plant Science and Life Sciences.
Professionals: Resident Doctors, Biotechnology, Bioinformatics, Medicine and Pharmaceutical scientists from industry, academia, and regulatory agencies. Hands-on exercises will be performed individually using software tools on your own laptops. (no prior experience required).

T & C
  • It is recommended to provide GMAIL email address.
  • Video recording of each session will be provided at the end of the session to give the user a unique learning experience.
  • Interactive training sessions will be conducted on Google Meet/Zoom so to give users a better learning experience.
  • As it is with a LIVE TRAINER hence practical application, i.e., the experiments/tasks to be performed can be done in the best explainable manner.
  • In this Online Workshop, there will be a LIVE trainer who will solve queries along with training.
  • Make sure you register under the right category. If you register under the wrong category then your registration will be invalid and NO REFUND WILL BE MADE IN THIS CASE. This is your mistake and the company is not responsible for it.
  • To avoid this do read the description of the ticket before selecting and proceeding with payment.
  • You need to upload your professional ID which can be your Student ID Card or Research Institute ID Card or Company ID Card.
  • The certificate will be issued as per the details which you provide in the registration form while registering before payment.
  • Once you register relax we will send you the meeting link after the workshop registration gets over.
  • The program is SELF-PACED.
  • After each session video of that particular session will be shared with you so you can go through as many times as you want and perfect yourself in the topics & tasks.
  • If you miss any session then NO PROBLEM you can still perform the tasks by going through the video of that particular session. 
  • We want to make sure that you learn properly hence the training certificate will be given ONLY on successful completion of all the tasks given by the trainer.
  • The certificates of all our Online programs are sent by email(softcopy) which has a unique barcode. You can take a print of that on heavy cardstock or photo paper and get it laminated if required.
  • The registration is NON-REFUNDABLE and NON-TRANSFERABLE.
  • BDG Lifesciences (OPC) Pvt. Ltd., India reserves the right of admission in all our programs.
  • If you are removed or your registration is canceled then there will be no answer to that. We have our own reasons for such an act of ours
  • If we do not wish to give this workshop to any participant then we will refund their amount.

Venue

This is an online event
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About
BDG LifeSciences (OPC) Pvt. Ltd. is a Bioinformatics company and are into business since 2010. We are an expert in conducting Training, Novel Research Projects, Workshops & Online Courses in technologies of Bioinformatics.We have a strong experience of 500+ Workshops & 60+ International publications
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Send your queries to the event organizer
BDG Lifesciences (OPC) Pvt. Ltd. profile image
CONTACT ORGANIZER
Have a question?
Send your queries to the event organizer
BDG Lifesciences (OPC) Pvt. Ltd. profile image
CONTACT ORGANIZER
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