One Day Workshop on Computational Chemistry and Bio-molecular Simulations December 9, 2013 School of Chemical & Biotechnology
biosheeba87
Introduction
Twentieth century has undoubtedly been a golden age for technology and one of the main reasons behind this is the invention and the rapid improvisation in computational machines and tools. Thanks to the rapid growth in the field of computers that today in silico research is an inevitable tool in most of the cutting-edge areas ranging from pharmaceuticals to missile technology. Needless to say, today all the leading pharmaceutical companies as well as research labs are well equipped with computational tools/. It is not only economical to carry out the preliminary research in silico prior to implementing it in real, the myriads of trials that is plausible in computational space is the primary advantage. This is amply exploited in drug discovery research where several targets are screened effectively prior to arriving at possible right hits. There are various computational tools in pharmaceuticals research that are currently in vogue and most of them are based on the principles of quantum chemistry, molecular dynamics or Monte-Carlo simulations.
In this workshop we will introduce the basics of the above mentioned techniques namely quantum chemistry, molecular dynamics and Monte-Carlo simulations. We will introduce electronic structure calculations of molecules, the heart of quantum chemistry, through Gaussian suite of program. For all the three techniques, we will introduce the basic conceptual framework in which they are constructed, the way they are executed through the software tools and finally highlight few wide applications that can be readily realized using these techniques. In this workshop we will also have a hands-on session where we would carry out some basic calculations and simulations and analyze the result. We hope that this introductory workshop would help you gauge the depth and application of computational research and instill some interest to pursue it further.
Session Details
|
| ||
| 09.00 Hr – 9.05 Hr | Introduction | |
| 09.05 Hr – 10.00 Hr | Abinitio Quantum Chemistry | Dr. V. Ramanathan |
| 10.00 Hr – 11.00 Hr | Monte Carlo Simulations | Dr. S. Arunachalam |
| 11.00 Hr – 12.00 Hr | Molecular dynamics simulations | Dr. R. Vigneshwar |
| 12.00 Hr – 13.00 Hr | Lunch | |
|
| ||
| 13.00 Hr – 14.00 Hr | QM hands-on | |
| 14.00 Hr – 15.00 Hr | MC Simulation hands on | |
| 15.00 Hr – 16.00 Hr | MD Simulation hands on | |
| 16.00 Hr – 16.45 Hr | Interactive and Feedback Session | |
| 16.45 Hr – 17.00 Hr | Closing Note and Acknowledgements | |
Outline of Sessions Content
Lecture 1: Ab initio Quantum Chemistry
Speaker: Dr. V. Ramanathan
Title: Introduction to Electronic structure theory and calculations using Gaussian
Broad outline of the lecture:
- Ab initio - Hartree Fock method
- Ab initio - post Hartree-Fock methods
- Density Funcational method
- Introduction to Gaussian software
- Input methods (z-matrix, xyz coordiantes)
- Geometry optimization and Frequency calculation
- Analysing the output file.
Hands on:
- writing z-matrix for a H2O and CH4 manually
- generating the z-matrix using a different software
- optimising the structure of water dimer
- scanning the potential of 1,2, dichloroethane
Lecture 2: Monte Carlo Simulations
Speaker: Dr. S. Arunachalam
Title: Monte Carlo (MC) minimization and conformational search
Broad Outline of the lecture:
- What is Monte Carlo method
- Probability distributions and Sampling
- Metropolis Algorithm for MC simulation
- Applications of MC simulation
- Hands on training for conformational search of a small polypeptide using TINKER
Lecture 3: Molecular dynamics simulations
Speaker: Dr. R. Vigneshwar
Title: Introduction to Molecular Dynamics Simulations
Broad outline of the lecture:
- Why molecular dynamics? – Advantages over statistical approach
- Newton’s equation of motion
- Force fields, inter-atomic potentials and truncation
- Boundary conditions and minimum image convention
- Integration: Verlet algorithm and the leap frog algorithm
- Steps in molecular dynamics simulations using GROMACS
- Some examples of the uses of MD simulations
Hands on
MD Simulations and Analysis:
Preparing a protein system (Lysozyme) for simulation in GROMACS.
- Centering the structure in a box
- Solvation of the structure.
- Adding counterions
- Creating the MD parameter file.
- Submitting the job for simulations.
Analysis of the MD trajectory
- RMSD calculation
- RMSF calculation
- Energy and temperature calculations.
- Radius of gyration
Registration
- Registration (and attending) for the workshop is absolutely free of cost.
- Those interested may kindly send an email expressing willingness to attend the workshop to the email ids given in the 'Contact Us' page. Please write CCBMS in the subject of the e-mail.
aravind.setti
sasikala
This is Sasikala.Im really interest in "One Day Workshop on Computational Chemistry and Bio-
molecular Simulations December 9, 2013 School of Chemical & Biotechnology".But i need the venue
details.please let me know.
Thanking you
With Regards,
SASIKALA RAJENDRAN
ABBOTT HEALTHCARE PVT LTD.,
EMPLOYEE CODE:717504,
KAM-DIABETES TASK FORCE,
HQ: CHENNAI
MOBILE:8056282204
MAIL ID: sas...@rediffmail.com
 |
Get your own FREE website, FREE domain & FREE mobile app with Company email. | Know More > |
Boopalan Bhagavan
--
For BioVeritaz/Secretariat
BioVeritaz Organization: http://www.bioveritaz.org
Join BioVeritaz Organization. Reach us at
Googlegroups: https://groups.google.com/d/forum/bioveritaz
--
BioVeritaz is for Biological scientistsbased on Indian origin.
We respect your privacy. Should you feel you are not interested, please unsubscribe from the googlegroup. Alternatively, you can send a request to the moderator.
---
You received this message because you are subscribed to the Google Groups "Bioveritaz" group.
---
You received this message because you are subscribed to the Google Groups "BioVeritaz" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bioveritaz+...@googlegroups.com.
To post to this group, send email to biove...@googlegroups.com.
Visit this group at http://groups.google.com/group/bioveritaz.
To view this discussion on the web visit https://groups.google.com/d/msgid/bioveritaz/CAL%2BirSU1iJV0odDwpt57_UjGtQCeYMN4bOEzMV3aqKNMW94NkQ%40mail.gmail.com.
For more options, visit https://groups.google.com/groups/opt_out.
Boopalan Bhagavan
Assembling at 8.45 am in Jiva Chaitanya Building (JVC; School of Chemical and Biotechnology building) entrance lobby
Sessions at Bio-informatic labs in JVC 3rd floor.--
For BioVeritaz/Secretariat
BioVeritaz Organization: http://www.bioveritaz.org
Join BioVeritaz Organization. Reach us at
Googlegroups: https://groups.google.com/d/forum/bioveritaz
--
BioVeritaz is for Biological scientistsbased on Indian origin.
We respect your privacy. Should you feel you are not interested, please unsubscribe from the googlegroup. Alternatively, you can send a request to the moderator.
---
You received this message because you are subscribed to the Google Groups "Bioveritaz" group.
---
You received this message because you are subscribed to the Google Groups "BioVeritaz" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bioveritaz+...@googlegroups.com.
To post to this group, send email to biove...@googlegroups.com.
Visit this group at http://groups.google.com/group/bioveritaz.
To view this discussion on the web visit https://groups.google.com/d/msgid/bioveritaz/52a49e5f.41a0420a.0ea3.ffffe2aaSMTPIN_ADDED_BROKEN%40gmr-mx.google.com.
philomena george
--
For BioVeritaz/Secretariat
BioVeritaz Organization: http://www.bioveritaz.org
Join BioVeritaz Organization. Reach us at
Googlegroups: https://groups.google.com/d/forum/bioveritaz
--
BioVeritaz is for Biological scientistsbased on Indian origin.
We respect your privacy. Should you feel you are not interested, please unsubscribe from the googlegroup. Alternatively, you can send a request to the moderator.
---
You received this message because you are subscribed to the Google Groups "Bioveritaz" group.
---
You received this message because you are subscribed to the Google Groups "BioVeritaz" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bioveritaz+...@googlegroups.com.
To post to this group, send email to biove...@googlegroups.com.
Visit this group at http://groups.google.com/group/bioveritaz.
To view this discussion on the web visit https://groups.google.com/d/msgid/bioveritaz/52a49e5f.41a0420a.0ea3.ffffe2aaSMTPIN_ADDED_BROKEN%40gmr-mx.google.com.
For more options, visit https://groups.google.com/groups/opt_out.
--
With best regards,
Thanking you,
Yours truly,
* Dr. PHILOMENA GEORGE, M.Sc.,B.Ed.,Ph.D.,PGDHE.,FIBR, FNABS.,FSAB.,FMSF., FISCA.
**Professor& Former Head,
Biotechnology Department
Karunya University , Coimbatore-641114, Tamil Nadu
phil...@karunya.edu, drphi...@gmail.com, drphi...@yahoo.co.in
**Mobile +91 9600898379 : Office - 0422-2614471: *
*Fax ; 91 422 2615615, *website ; www.karunya.edu