[gmx-users] g_rmsf and pbc

[David van der Spoel]

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
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++