56 ms·
Fourier methods are good, but only when your potential is decaying slowly. If it decays fast, like van der Waals interaction which are plentiful in MD, you just
by semi-extrinsic 10y ago
Fourier methods are good, but only when your potential is decaying slowly. If it decays fast, like van der Waals interaction which are plentiful in MD, you just have to do the plain n-body approx.
- dekhn 10y agoIn MD, it's a combination of VDW and electrostatic. Typically VDW is just a cutoff (VDW forces beyond 8A are neglible), and electrostatic is handled by particle-mesh ewald. I worked on DNA and RNA, which have strong electrostatic interactions and my thesis work showed PME was critical for stability.
- semi-extrinsic 10y agoThis was what I was trying to say. Actually, this assumes atomistic MD where you have electrostatics. I've done some work with coarse-grained MD, where you've averaged out the electrostatics and you just have VDW.