Feature - Grids work like a CHARMM for molecular dynamics
In 1963, Richard Feynman said that “everything that living things do can be understood in terms of the jiggling and wiggling of atoms.” (1)
Molecular dynamics aims to better understand these jiggles and wiggles, using numerical methods to simulate the ways in which atoms and molecules move.
One tool facilitating this work is CHARMM—or Chemistry at HARvard Macromolecular Mechanics—a software application developed at Harvard University for modeling the structure and behavior of molecular systems.
CHARMM has multiple applications, but for Ana Damjanovic of the National Institutes of Health and Johns Hopkins University in Baltimore, Maryland, U.S., molecular dynamics simulations are the name of the game.
Damjanovic is using CHARMM to help her learn more about the interactions between proteins and water, an understanding of which can ultimately aid the design of medicinal drugs.
“I’m running many different simulations to determine how much water exists inside proteins and whether these water molecules can influence the proteins,” Damjanovic says.
“Water in protein interiors can play important functional roles—such as in enzymatic catalysis or charge transfer reactions—and when a protein moves, it can shift the position of these water molecules.”
“One of the bottlenecks in simulating how proteins function is that many functionally important motions occur on timescales of microseconds and longer, but molecular dynamics simulations can only sample real-time in nanoseconds,” Damjanovic says. “Sometimes even the processes that occur on nanosecond timescales, such as water penetration in some proteins, are not sampled properly with only a few simulations. To get better statistics, one needs to run many, many different simulations.”
This is where it pays to have access to grid computing, which provides the large number of processors necessary to obtain meaningful sampling.
Using your CHARMM on grids
“We have developed workflow management software for submitting and babysitting the jobs,” Miller explains. “Since molecular dynamics jobs usually take days to complete, and Open Science Grid sites are optimized for shorter jobs, each long job is split into many, many little jobs.”
“Now our workflow software can keep track of the rather large number of jobs—what’s submitted and what’s left to be done—and it can then automatically submit the work that’s to be done,” Miller says. “If a job fails, this is detected and the job is then resubmitted. There are multiple threads running as well, and they can branch out and run two different types of analysis on the same structure.”
Damjanovic says her access to Open Science Grid with the newly developed workflow software has worked like a charm.
“All I had to do is initially submit my simulations,” she says. “A month later, I had statistical analysis of lots and lots of simulation. No pain, and no babysitting.”
- Jen Nahn, Open Science Grid
This story also appeared as an OSG Research Highlight.