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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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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