[gmx-users] reference structure of g_rms

[Hsin-Lin Chiang]

Hi,

I got confused about the choice of reference structure of g_rms. (g_rms -s)
For example,
I run MD after PR.
That's means md.tpr was generated from pr.gro
I tried to use pr.gro and md.tpr to be the reference structure but get 
different result.
I think these two should cause the same result.
Could someone tell me  what cause the different and which choice is better?

And my version is gromacs v4.0.5

Sincerely yours,
Hsin-Lin