[gmx-users] g_mindist after trjconv -fit give different results

[eladp at post.tau.ac.il]

Hi all,

I have a system of protein+water+ions.
I measured the minimum distance between one of the ions to the protein.

Afterwards I fitted the trajectory using g_trjconv -fit rot+trans

Did the same mindist again and the graphs are not always identical.

Any suggestions?

I use gromacs 4.0.5 with an octahedron box.
same problem happens when I do trjconv -fit rot but does not happen  
when -fit trans.

In VMD I do see a difference in the position of the ion relative to  
the protein.

Thanks.
Elad P.