[gmx-users] (no subject)

[Attila Borics]

Hi,

I tried to use g_rms to analyze my trajectory, but I got really weird results.
g_rms -h says, that each structure from the trajectory is compared to a reference structure, wich is taken from the .tpr file. I ran g_rms on my trajectory, and I got very high RMSD values (0.5nm) even the first (starting) structure of my trajectory. I chopped out my starting structure from the trajectory and and calculated its RMSD compared to the .pdb file I used for input generation (pdb2gmx, and grompp) previously. The result was 0.0 in contrast with 0.5098, what g_rms yielded for the same structure (and what doesn't make any sense).
So there is a problem with g_rms, or I just did something wrong.
There's one little thing with the usage of g_rms, which is a bit fuzzy for me, so I try to describe what I did.

g_rms -s xxxxx.tpr -f xxxxx.xtc -n index.ndx -o rmsd

Select group for least squares fit

Group     4 (    Backbone) has   603 elements

How many groups do you want to compare ? 1
OK. I will compare 1 groups

Group     4 (    Backbone) has   603 elements


So as I believe I just fitted the backbone of each structure in my trajectory to the backbone of reference structure and calculated RMSD for each. Is that right?
Or I just misunderstood something?
Thanks in advance. 

Attila