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Replaying a Lammps Trajectory

EDIT: Turns out I just didn't google the correct words, LAMMPS does have one. It's the command rerun. Oops.

LAMMPS, the molecular dynamics engine, doesn't have a replay function allowing one to go back and calculate properties on a trajectory, especially forces and energies. This came up in my work and I got started on writing some new LAMMPS code to accomplish this. I wanted to be able to calculate forces with a different potential on a trajectory. Anyway, I realized you can accomplish this just by using the LAMMPS looping variables. No new code necessary. It can be done by using the read_dump command to load particular trajectory frame. A sample input script is below

Predicting the Future of Simulations

In my day job, molecular modeling, I simulate the position and velocity of every atom in biological molecules. As you can imagine, doing this yields nearly complete information about whatever biological system I'm studying and allows me to predict the behavior of proteins. Well, that's the theory. It's more complex than that and often fails spectacularly in practice. Ignore that for now. Let's focus on the systems that can be simulated. In 1982 CHARMM, one the first molecular dynamics tool capable of simulating tiny proteins, was released. It was possible to simulate a small protein for one tenth of one billionth of one second. Now we can simulate a protein for one thousandth of a second. That's an increase of 10^7 in the speed of molecular simulations in about 30 years. In 1990, we were able to simulate lysozyme, a small protein, for few billionths of a seconds. Now we can simulate a virus for a few billionths of a second. That's an increase in about 10^4 mass of molecular simulations in 30 years. Assuming continued exponential growth (see plots below), here are my upcoming interesting milestones in computer simulation

Year	Event
2023	The first simulation of every atom in a ribosome for 10 milliseconds
2038	The first simulation of every atom in a virus for 1 second
2131	The first simulation of every atom of a cell for 1 hour
2191	We can simulate every atom of every cell in a heart for 1 heartbeat
2227	Every atom of every cell in a human brain can be simulated as fast they move in a human brain