[lammps-users] DOF, fix rigid and fix shake

I have some questions regarding dof and some fixes. If any of you have some insights, plz give me some information.

  1. when using fix rigid at N2H4 molecules which has gauche conformation (not linear), lammps computes their dof automatically. I computed ke and temp, manually calculated dof according to KE = 0.5kT*dof. In case of 22 N2H4, dof equals 129. In case of 14 N2H4, dof equals 81. My simulation is 3D, so dof should be 3n-6. However, it looks like Lammps used 3n-3. (with 3n-3, we can get relation between number of N2H4 and dof. Namely, 14 N2H4 à n=28, 22 N2H4 à n=44…… which looks like one N2H4 equals to n=2)

In addition, at above case, N2H4 is composed of 6 molecules, but fix rigid reduced dof to n=2. Is there any specific rule to determine n when using fix rigid for nonlinear molecules?

  1. when water (using fix shake) is simulated with some N2H4 molecules (using fix rigid), I found that dof of water is messed up, related with dof of hydrazine. Assuming that 3n-3 used for dof whether it’s right or wrong anyhow, bellows are some cases of messed dof. (I printed out ke and temp of water only, and calculated dof)

System0: 250H2O à dof of water = 1497 à n = (1497+3)/3 = 500, which is 250*2

System1:1Hydrazine + 38H2O à dof of water = 231 à n = (231+3)/3 = 78, which is 12 + 382

System2:14Hydrazine + 14H2O à dof of water = 165 à n = (165+3)/3 = 56, which is 142 + 142

It looks like dof of water is sum of dof of water and hydrazine.

As a result, when I see the movies of system1 and system2, water molecules of system2 moves much faster than system1 because more undesired dof is added in system2.