[gmx-users] g_rms, g_rmsdist, g_rmsf

[Arturas]

Hello,

I have some trivial questions here. Guess they are discussed before in
a part. I checked the manual but there is some misunderstanding still.

1. I need to calculate the distance over all trajectory between two
atoms. How to do that ? Is there any third party software (graphical
?) to manipulate such analysis easy ? I check that 'g_rmsf' and
'g_rmsdist' could be useful, but I am not sure...

2. I have my trajectory file and my reference file (e.g. pdb). The
reference file has structure, which is analogous to ONE GROUP in my
modeling system. I need to have RMSD of all recorded steps in my
trajectory against my reference structure. Can 'g_rms' help me ?
However, there is written in the manual that g_rms calculates RMSD
against all modeling system. 

g_rms has some options that are quite unclear. What means option -f2
'other structure' ?

With best
Arturas