###Atomistic Modeling for Small-Angle Scattering ‹ A Short Course
#####May 26-28, 2015
#####Institut Laue-Langevin, Grenoble, France
Molecular simulation is an important technique to analyze and interpret
molecular phenomena across many disciplines. Small-angle scattering (SAS)
utilizing either X-ray or neutron sources is a valuable method to
characterize shape, interactions, and properties of many soft-matter
systems. Modeling of SAS data is typically done using analytical
functions and/or dummy-ball (DB) models. While these methods are simple,
they have proven to be quite robust and have allowed for a tremendous
expansion of SAS studies to a wide variety of systems. Atomistic modeling
can be used to interpret SAS data and inherently provides structural and
physical knowledge that are unavailable using analytical or DB models. In
additional, atomistic models can allow the use of experimental and
computational constraints on the SAS data.
The goal of this three day introductory course is to use modern
simulation methods and software tools to predict and analyze small-angle
scattering data of soft-matter systems, focussing particularly on
biological systems. Participants will be familiarized with SASSIE, a
software framework designed to facility the use of atomistic modeling to
interpret scattering data. SASSIE-web, a product of the CCP-SAS
consortium, will be the primary tool used during the course and will be
freely available to the community after the course.
The course will involve a mixture of lectures and examples with student
lessons. Examples will involve various protein, dna, and their complexes.
The emphasis will be on structure building, ensemble molecular
simulation, calculation of scattering profiles and comparison to
experimental data.
Day 1: Introduction to molecular modeling using force-fields and SASSIE
Day 2: Intermediate MD, SASSIE and student projects.
Day 3: Advanced SASSIE and student projects.
Students are encouraged to contact the course organizers in advance to
discuss their systems as a portion of the course will involve helping
students set-up and model their project.
---
###NOTE: Files to carry out the labs are no longer available below. Please see more recent courses for updated labs and files.
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####Tuesday 5/26/2015
| Time | Lead | Activity | File
| ------------- |--------|-------|------|
| 9:00 - 9:30 AM | JEC | Course Introduction | [lecture_0.pdf](files/lecture_0.pdf)
| 9:30 - 10:30 AM | JEC | Lecture 1: Coordinates to Structure | [lecture_1.pdf](files/lecture_1.pdf)
| 10:30 - 10:45 AM | | **Break**
| 10:45 - Noon | DWW/JEC/EHB | Lab 0: Software Installation & SASSIE-web | [lab_0.pdf](files/lab_0.pdf)
| Noon - 1:00 PM | | **Lunch** |
| 1:00 - 2:45 PM | DWW/HZ/EHB | Lab I: VMD and PDB Scan | [lab_I.pdf](files/lab_I.pdf)
| 2:45 - 3:00 PM | | **Break**
| 3:00 - 5:00 PM | DWW/HZ/EHB | Lab II: PSFGEN/NAMD | [lab_II.pdf](files/lab_II.pdf)
---
####Wednesday 5/27/2015
| Time | Lead | Activity | File
| ------------- |--------|-------|------|
| 9:00 - 10:00 AM | JEC | Lecture 2: MD II | [lecture_2.pdf](files/lecture_2.pdf)
| 10:00 - 10:15 AM | | **Break**
| 10:15 - Noon | DWW/HZ/EHB | Lab III: NAMD | [lab_III.pdf](files/lab_III.pdf)
| Noon - 1:00 PM | | **Lunch** |
| 1:00 - 1:30 PM | JEC | Lecture 3: MMC & SASSIE Overview | [lecture_3.pdf](files/lecture_3.pdf)
| 1:30 - 3:00 PM | DWW/HZ/EHB | Lab IV: SASSIE-web Quick Start | [lab_IV.pdf](files/lab_IV.pdf)
| 3:00 - 3:15 PM | | **Break**
| 3:00 - 4:00 PM | DWW/HZ/EHB | Lab V: SASSIE-web Analysis | [lab_V.pdf](files/lab_V.pdf)
| 4:00 - 5:00 PM | ALL | Breakout sessions for student projects | -
---
####Thursday 5/28/2015
| Time | Lead | Activity | File
| ------------- |--------|-------|------|
| 9:00 - 10:15 AM | DWW/HZ | Lab VI: Advanced SASSIE-web | [lab_VI.pdf](files/lab_VI.pdf)
| 10:15 - 10:30 AM | | **Break**
| 10:30 - 10:45 AM | JEC | Lecture 4: Advanced Building | [lecture_4.pdf](files/lecture_4.pdf)
| 10:30 - Noon | DWW | Lab VII: Advanced Building | [lab_VII.pdf](files/lab_VII.pdf)
| Noon - 1:00 PM | | **Lunch** |
| 1:00 - 2:45 PM | ALL | Lab VIII: Breakout sessions for student projects | -
| 2:45 - 3:00 PM | | **Break**
| 3:00 - 5:00 PM | ALL | Lab IX: Breakout sessions for student projects | -
---
###[SASSIE-web: Quick Start](sassie-web-quick-start/quick-start.html)
###[How to Use Visual Molecular Dynamics (VMD)](vmd/vmd.html)
###[Build](http://sassie-web.chem.utk.edu/docs/build/build.html)
###[PDB Scan](build/pdbscan/pdbscan.html)
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