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 atomic interactions 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 gain experience with modern simulation tools such as VMD, NAMD. The latter half of the course will introduce SASSIE, a software framework designed to facility the use of atomistic modeling to interpret scattering data.
The course will involve a mixture of lectures and examples with student lessons. Examples will involve various protein, dna, and their complexes. Advanced simulation methods for glycosylated proteins, lipidic systems and coarse-grain methods can be accommodated depending on demand. 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
Day 2: Intermediate MD, SASSIE and advanced building methods.
Day 3: Advanced MS, 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 initial models for their own projects.
| Time | Lead | Activity | File |
|---|---|---|---|
| 9:00 - 9:30 AM | JEC | Course Introduction | lecture_0.pdf |
| 9:30 - 10:30 AM | JEC | Lecture 1: Coordinates to Structure | lecture_1.pdf |
| 10:30 - 10:45 AM | Break | ||
| 10:45 - Noon | ALL | Lab 0: Software Installation and SASSIE-web Basics | lab_0.pdf; basicosxlinux_commands.pdf; basicwindowscommands.pdf |
| Noon - 1:00 PM | Lunch | ||
| 1:00 - 2:45 PM | SK/ALL | Lab I: VMD | lab_I.pdf |
| 2:45 - 3:00 PM | Break | ||
| 3:00 - 5:00 PM | SK/ALL | Lab II: PSFGEN/NAMD | labIIosx_linux.pdf; labIIwindows.pdf |
| Time | Lead | Activity | File |
|---|---|---|---|
| 9:00 - 10:00 AM | JEC | Lecture 2: MD II | lecture_2.pdf |
| 10:00 - 10:15 AM | Break | ||
| 10:15 - Noon | SB/CJ | Lab III: NAMD | labIIIosx_linux.pdf labIIIwindows.pdf |
| Noon - 1:00 PM | Lunch | ||
| 1:00 - 1:30 PM | JEC | Lecture 3: MMC & SASSIE Overview | lecture_3.pdf |
| 1:30 - 3:00 PM | SK/ALL | Lab IV: SASSIE-web Quick Start | lab_IV.pdf |
| 3:00 - 3:15 PM | Break | ||
| 3:15 - 5:00 PM | SK/ALL | Lab V: SASSIE-web Workflows | lab_V.pdf |
| Time | Lead | Activity | File |
|---|---|---|---|
| 9:00 - 9:30 AM | SCH | Lecture 4: Advanced SASSIE-web | lecture_4.pdf |
| 9:30 - 10:00 AM | SCH/CJ | Lab VI-1: Advanced SASSIE-web | lab_VI.pdf lab_VI.html |
| 10:00 - 10:15 AM | Break | ||
| 10:15 - 11:30 AM | SCH/CJ | Lab VI-2: Advanced SASSIE-web | lab_VI.pdf |
| 11:30 - Noon AM | JEC | Lecture 5: Advanced Structure Building | lecture_5.pdf |
| Noon - 1:00 PM | Lunch | ||
| 1:00 - 3:00 PM | SK/ALL | Lab VII: Advanced Structure Building | labVIIosx_linux.pdf labVIIwindows.pdf |
| 3:00 - 3:15 PM | Break | ||
| 3:15 - 5:00 PM | SB/ALL | Lab VIII: Breakout Sessions: Student Projects and Advanced MD Labs | labVIIImembrane_builder.pdf labVIIInormal_modes.pdf |