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

- 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 = 0.5
*k*T*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?

- 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 1*2 + 38*2

System2:14Hydrazine + 14H2O à dof of water = 165 à n = (165+3)/3 = 56, which is 14*2 + 14*2

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.