Computational Biophysics Workshop - Bangalore, Nov. 6-16, 2007
Program
Below is the program of the workshop as taken from the CCMS program posted at the workshop website.
Day 1 Nov 6, 2007, Tuesday
08:00 : Bus from JRD Tata Memorial Library, IISc to JNCASR
08:30 - 09:30: Registration and Breakfast
Lectures :
09:30-10:00 : Introduction to workshop (MRS Rao)
10:00-11:15 : Introduction to protein structure and dynamics: What can we learn from simulations? (Saraswathi Vishveshwara)
11:15-11:30 : Tea
11:30-12:45 : DNA Structure and Dynamics - as revealed by crystallography and MD Simulations.(Manju Bansal)
12:45-14:00 : Lunch
Hands-on-session:
14:00-16:00 : Introduction to protein data bank (Vani Vemparala)
16:00-16:30 : Tea
16:30-18:00 : Introduction to VMD (Vani Vemparala)
18:15 : Bus from JNCASR to IISc Campus
Day 2 Nov 7, 2007, Wednesday
08:15 : Bus from JRD Tata Memorial Library, IISc to JNCASR
08:45-09:30: Breakfast
Lectures :
09:30-11:00 : Scripting & TCL - I (A. Kohlmeyer)
11:00-11:15 : Tea
11:15-12:45 : Computational statistical mechanics(S. Balasubramanian)
12:45-14:00 : Lunch
Hands-on-session:
14:00-16:00 : TCL scripts (A. Kohlmeyer)
16:00-16:30 : Tea
16:30-18:00 : VMD (cont.,) (Aruna Rajan)
18:15 : Bus from JNCASR to IISc Campus
Day 3 Nov 8, 2007, Thursday
08:15 : Bus from JRD Tata Memorial Library, IISc to JNCASR
08:45-09:30: Breakfast
Lectures :
09:30-11:00 : Introduction to simulation methodologies (Srikanth Sastry)
11:00-11:15 : Tea
11:15-12:45 : Scripting & TCL - II (A. Kohlmeyer)
12:45-14:00 : Lunch
Hands-on-session:
14:00-16:00 : VMD (cont.,) (Aruna Rajan)
16:00-16:30 : Tea
16:30-18:00 : Shell scripts (A. Kohlmeyer)
18:15 : Bus from JNCASR to IISc Campus
Day 4 Nov 9, 2007, Friday
08:15 : Bus from JRD Tata Memorial Library, IISc to JNCASR
08:45-09:30: Breakfast
Lectures :
09:30-11:00 : Introduction to force fields (Vani Vemparala)
11:00-11:15 : Tea
11:15-12:45 : Length & time scales; MD implementation (Prabal Maiti)
12:45-14:00 : Lunch
Hands-on-session:
14:00-16:00 : Introduction to NAMD (Aruna Rajan)
16:00-16:30 : Tea
16:30-18:00 : NAMD (cont.,)(Aruna Rajan)
18:15 : Bus from JNCASR to IISc Campus
19:30 : Banquet Dinner at JVH Lawns
Day 5 Nov 10, 2007, Saturday
08:15 : Bus from JRD Tata Memorial Library, IISc to JNCASR
08:45-09:30: Breakfast
Lectures :
09:30-11:00 : Ewald & Particle mesh Ewald (Prabal Maiti)
11:00-11:15 : Tea
11:15-12:45 : Introduction to VMD scripts (A. Kohlmeyer)
12:45-14:00 : Lunch
Hands-on-session:
14:00-15:45 : NAMD (cont.,) (Aruna Rajan)
15:45-16:45 : Tea + Poster Session
16:45-18:00 : NAMD (cont.,)(Vani Vemparala)
18:15 : Bus from JNCASR to IISc Campus
Nov 11, 2007, Sunday
Day off
Day 6 Nov 12, 2007, Monday
08:15 : Bus from JRD Tata Memorial Library, IISc to JNCASR
08:45-09:30: Breakfast
Lectures :
09:30-11:00 : Langevin dynamics, constraints (Srikanth Sastry)
11:00-11:15 : Tea
11:15-12:45 : Introduction to VMD scripts-2 (A. Kohlmeyer)
12:45-14:00 : Lunch
Hands-on-session:
14:00-16:00 : PSF files (Vani Vemparala)
16:00-16:30 : Tea
16:30-18:00 : Topology tutorials (cont.,)(Vani Vemparala)
18:15 : Bus from JNCASR to IISc Campus
Day 7 Nov 13, 2007, Tuesday
08:15 : Bus from JRD Tata Memorial Library, IISc to JNCASR
08:45-09:30: Breakfast
Lectures :
09:30-10:30 : Membranes & membrane proteins (Vani Vemparala)
10:30-11:30 : Coarse grained simulations of lipid membranes with and without water(P. B. Sunil Kumar)
11:30-11:45 : Tea
11:45-12:45 : Coarse Grained MD Parametrization and Application to Peptide Nanotube Formation (A. Kohlmeyer)
12:45-14:00 : Lunch
Hands-on-session:
14:00-15:45 : Membrane simulation (Vani Vemparala)
15:45-16:45 : Tea + Poster Session
16:45-18:00 : Membrane simulation (Vani Vemparala)
18:15 : Bus from JNCASR to IISc Campus
Day 8 Nov 14, 2007, Wednesday
08:15 : Bus from JRD Tata Memorial Library, IISc to JNCASR
08:45-09:30: Breakfast
Lectures :
09:30-10:30 : Simulating Lipid Membranes using Dissipative Particle Dynamics (P. B. Sunil Kumar)
10:30-11:30 : DNA helical parameters (Dhananjay Bhattacharyya)
11:30-11:45 : Tea
11:45-12:45 : MD Simulations of Nucleic Acids (Dhananjay Bhattacharyya)
12:45-14:00 : Lunch
Hands-on-session:
14:00-16:00 : Helical parameters using NUPARM (Dhananjay Bhattacharyya)
16:00-16:30 : Tea
16:30-18:00 : Analyzing DNA data (Dhananjay Bhattacharyya)
18:15 : Bus from JNCASR to IISc Campus
Day 9 Nov 15, 2007, Thursday
08:15 : Bus from JRD Tata Memorial Library, IISc to JNCASR
08:45-09:30: Breakfast
Lectures :
09:30-11:00 : Free energy, Jarzinsky’s equality (Srikanth Sastry)
11:00-11:15 : Tea
11:15-12:45 : Correlated movements in proteins in proteins: Insights from the dynamics of structure networks (Saraswathi Vishveshwara)
12:45-14:00 : Lunch
Hands-on-session:
14:00-16:00 : Steered molecular dynamics (Aruna Rajan)
16:00-16:30 : Tea
16:30-18:00 : SMD (cont.,)(Aruna Rajan)
18:15 : Bus from JNCASR to IISc Campus
Day 10 Nov 16, 2007, Friday
08:15 : Bus from JRD Tata Memorial Library, IISc to JNCASR
08:45-09:30: Breakfast
Lectures :
09:30-11:00 : Special lecture (Sanjib Senapati)
11:00-11:15 : Tea
11:15-11:25 : Closing Session
11:30-13:00 : Hands-on-Session
13:00-14:00 : Lunch
14:15 : Bus from JNCASR to IISc Campus
