[gmx-users] g_rmsf and pbc
Mark.Abraham at anu.edu.au
Tue Oct 23 16:43:48 CEST 2007
> 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?
GROMACS does an inexplicable segfault almost never. It's highly likely
that either there's more of an error message than you've said, or that
the problem is the result some catastrophic filesystem or OS issue.
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