GROMACS, VMD & NAMD 7 Day Certificate Online Hands-on Workshop

OPERATING SYSTEM
WINDOWS 10 WITH I3 OR ABOVE PROCESSOR

TOPICS
MD SIMULATION OF A PROTEIN USING NAMD -VMD ON WINDOWS
THEORY OF MD SIMULATION
INSTALLATION OF SOFTWARE
PREPARATION OF INPUT FILES
SOLVATION
SIMULATION IN PERIODIC BOUNDARY CONDITIONS
VMD ANALYSIS
PLOTTING THE DATA
MD SIMULATION OF A PROTEIN USING GROMACS
INSTALLATION OF UBUNTU(VIRTUAL BOX)
INSTALLATION OF GROMACS
PREPARATION OF INPUT FILES
SOLVATION
IONIZTION
MINIMIZATION
NPT EQILIBRATION PHASE 1
NVT EQUILIBRATION PHASE 2
VMD AND QTGRACE/XMGRACE ANALYSIS

PRACTICAL APPLICATION
DAY 1    
1.    THEORY OF MD SIMULATION
2.    INSTALLATION OF SOFTWARES
I)    NAMD
II)    VMD
III)    NAMD FILES
3.    WORKING IN CMD AND VMD TK CONSOLE THROUGH WORKING DIRECTORY
4.    PREPARATION OF APOPROTEIN

DAY 2                           
1.    LEARNING PGN SCRIPT
2.    RUNNING PSFGEN TO PREPARE INPUT PDB AND PSF FILES
3.    LEARNING INPUT FILES OF SIMULATION
I)    PDB
II)    PSF
III)    FORCE FIELD PARAMETER FILES
IV)    CONFIGURATION FILE

DAY 3:   
1. IMPORTANCE OF SOLVATION
2. SOLVATION IN WATER SPHERE
3. SOLVATION IN WATER BOX

DAY 4
4. RUNNING SIMULATION IN WATER SPHERE-NON PERIODIC BOUNDARY CONDITION
5. RUNNING SIMULATION IN WATER BOX-PERIODIC BOUNDARY CONDITION
6. PREPARATION OF OUTPUT FILES

DAY 5
1.    ANALYSIS OF SIMULATION FOR WATER SPHERE
2.    ANALYSIS OF SIMULATION FOR WATER BOX
3.    THEORY OF GROMACS
4.    INSTALLATION OF VIRTUAL BOX
5.    INSTALLATION OF GROMACS

DAY 6
1.    PREPARATION OF INPUT FILES
2.    SOLVATION
3.    IONIZATION

DAY 7:
1.    MINIMIZATION
2.    EQUILIBRATION
      NPT
      NVT
3.    ANALYSIS

• 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.