3 ms·

The beauty of CHARMM (at the time) was that it was the first practical combination of a forcefield and MD engine, that made it practical to simulation proteins.

by bbgm 13y ago

The beauty of CHARMM (at the time) was that it was the first practical combination of a forcefield and MD engine, that made it practical to simulation proteins. While other packages have left it behind on perf and capability, the forcefield itself remains very high quality, and the breadth of functionality is still as good as it gets. Unfortunately the implementation could do with an overhaul since it still looked like something from the early 80s (I haven't seen the CHARMM code in 5 years)

davecap1 13y ago
It's still mostly fortran :)
Xcelerate 13y ago
> the forcefield itself remains very high quality, and the breadth of functionality is still as good as it gets. It's kind of weird that forcefields haven't improved all that much. Implementation has improved drastically (LAMMPS, Gromacs, etc.) and QM level theory has too (FCIQMC, exploiting symmetries to eliminate the sign problem), but MD forcefields don't seem to have made a whole lot of progress from CHARMM, AMBER, and UFF. I suppose some of the reactive potentials (AIREBO and Tersoff) are a step up, but still...
- acadien 13y ago
  Maybe that's true for biological compounds, but for the rest of the periodic table new potentials are constantly being developed (and some may even be improvements). Semiconductors, transition metals, heavy elements, ferromagnetics, you name it... its being worked on. Actually even for biological molecules there are still advances being made. Water is an excellent example seeing how there is a new potential released once every 6 months or so. Its difficult to say whether these actually show a quantifiable improvement over old potentials, but its still an area of constant effort and progress.
  - Xcelerate 13y ago
    > whether these actually show a quantifiable improvement over old potentials Yeah, that's what I was meaning with regard to force-fields in general. What are we, like TIP23P for water now? ;)

by bbgm 13y ago

davecap1 13y ago

It's still mostly fortran :)

Xcelerate 13y ago

> the forcefield itself remains very high quality, and the breadth of functionality is still as good as it gets. It's kind of weird that forcefields haven't improved all that much. Implementation has improved drastically (LAMMPS, Gromacs, etc.) and QM level theory has too (FCIQMC, exploiting symmetries to eliminate the sign problem), but MD forcefields don't seem to have made a whole lot of progress from CHARMM, AMBER, and UFF. I suppose some of the reactive potentials (AIREBO and Tersoff) are a step up, but still...

acadien 13y ago
Maybe that's true for biological compounds, but for the rest of the periodic table new potentials are constantly being developed (and some may even be improvements). Semiconductors, transition metals, heavy elements, ferromagnetics, you name it... its being worked on. Actually even for biological molecules there are still advances being made. Water is an excellent example seeing how there is a new potential released once every 6 months or so. Its difficult to say whether these actually show a quantifiable improvement over old potentials, but its still an area of constant effort and progress.
- Xcelerate 13y ago
  > whether these actually show a quantifiable improvement over old potentials Yeah, that's what I was meaning with regard to force-fields in general. What are we, like TIP23P for water now? ;)