[gmx-users] g_rmsf and pbc

[tangxuan]

Dear all,
   The protein I am working on is rubisco, consisting of 8 identical
large subunits and 8 identical small subunits. I try to calculate RMSF
for each large subunits, but the rmsf values seems  much large to some
large subunits. So I check the first frame of the protein structutre,
and I found that these large subunits having large rmsf values seems
separate in the box. Then I tried to use trjconv -pbc nojump to remove
the jump for each of them in the xtc file. When I use new xtc file and
original tpr file to calculate the rmsf, it shows " Segmentation fault"
error. This may be because  the coordinators of atoms in the tpr file
are very diffrent from that in the fist frame. Do you know how to solve
this problem?

Thank you

Tang Jiaowei