[gmx-users] g_rmsf and pbc

[tangxuan]

Mark,thanks for your reply. I am not sure what happened and  I can show
you the error message,"
Group   101 (     chK_chM) has  4070 elements
Group   102 (     chM_chO) has  4070 elements
Group   103 (     chO_chI) has  4070 elements
Group   104 (     chJ_chL) has  4070 elements
Group   105 (     chL_chN) has  4070 elements
Group   106 (     chN_chP) has  4070 elements
Group   107 (     chP_chJ) has  4070 elements
Select a group: 22
Selected 22: 'chC'
Reading frame       1 time 20001.000   Segmentation fault
[miro:~/rubisco-2/chlamy_wt] % more chlamy_wt.xtc "
Thanks.
Tang jiaowei

On Wed, 2007-10-24 at 00:43 +1000, Mark Abraham wrote:
> tangxuan wrote:
> > 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.
> 
> Mark
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