[gmx-users] g_rmsf and pbc

[tangxuan]

I tried "trjconv -pbc nojump" to the whole protein and then calculated
the rmsf of the subunits. This method seems good to some separate
subunits, but  other separate subunits still have strange high rmsf
values. I try "trjconv -pbc mol" too, and i have got same results. In
this simulation,the subunits are separate in the first frame. Do you
have any other methods to solve this problem?

On Tue, 2007-10-23 at 17:18 +0200, David van der Spoel wrote:
> tangxuan wrote:
> > 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
> > 
> most likely the tpr and xtc files have different number of atoms.
> 
> as for your original problem, try trjconv -pbc mol in version 3.3.2
> 
> 
> > 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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