3 ms·
Molecules are tricky. They're obviously machines, but you're dealing with Quantum Mechanics if you go to first principles.
by JabavuAdams 10y ago
Molecules are tricky. They're obviously machines, but you're dealing with Quantum Mechanics if you go to first principles.
- dekhn 10y agoWhich is why, for nearly all simulations, you use Born-Oppenheimer approximation and molecular dynamics using force fields derived from QM, but without the full explicit QM treatment. This is fine because with only rare examples (as far as modern science knows), QM treatment is not necessary for most molecular machines.
- nonbel 10y agoI didn't realize that. It sounds like the same situation with astronomical simulations. General Relativity is too complicated so everyone uses Newtonian mechanics plus a fudge factor. I think it is odd that the two most cherished scientific theories are not actually used in practice to compare with data. Also, this got me wondering how they did this simulation, which lead me to this site: http://www.tapir.caltech.edu/~phopkins/Site/GIZMO.html http://www.tapir.caltech.edu/~phopkins/Site/GIZMO.html There is a lot of code.. but after a quick look at it I see Netwonian mechanics. From analytic_gravity.h: void GravAccel_StaticIsothermalSphere() { double ISO_M200=95.21; double ISO_R200=160.0; double ISO_Eps=0.1; double ISO_FRACTION=0.9; double r, m, dx, dy, dz; int i; for(i = FirstActiveParticle; i >= 0; i = NextActiveParticle[i]) { dx = P[i].Pos[0]; dy = P[i].Pos[1]; dz = P[i].Pos[2]; r = sqrt(dx * dx + dy * dy + dz * dz); if(r > ISO_R200) m = ISO_M200; else m = ISO_M200 * r / ISO_R200; m *= ISO_FRACTION; if(r > 0) { P[i].GravAccel[0] += -All.G * m * dx / r / (r * r + ISO_Eps * ISO_Eps); P[i].GravAccel[1] += -All.G * m * dy / r / (r * r + ISO_Eps * ISO_Eps); P[i].GravAccel[2] += -All.G * m * dz / r / (r * r + ISO_Eps * ISO_Eps); } } }
- dekhn 10y agoYes, both astrophysics codes and MD are basically "n-body approximations" https://en.wikipedia.org/wiki/N-body_simulation https://en.wikipedia.org/wiki/N-body_simulation although if I understand correctly universal simulations do explicitly model general relatively Personally I find the "particle mesh". If you model the N-body calculation this way, you can solve for the field (potential) by converting to fourier space, doing some FFTs (which computers are really, really good at), then converting back to real space. This works in both astro and molecular simulations, really well.
- semi-extrinsic 10y agoFourier 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.
- Florin_Andrei 10y ago> QM treatment is not necessary for most molecular machines Still largely true, but more exceptions are being found all the time.
- dekhn 10y agoDo you mean, to simulate the active site of an enzyme, or that people are trying to explicitly model known quantum biology, like photosynthetic centers? I don't know that anybody is claiming it's necessary for protein folding or DNA/RNA simulations.