Hi CarstenI checked again and the segmentation fault appears to be unrelated to 
file size.  I obtained theeigenvector.trr files that give a seg fault using the 
g_covar -nofit option as I had already fit the datausing trjconv -fit 
rot+trans.  This would mean the reference structure file is not saved in the 
.trr file.  Also, these eigenvector.trr files were generated using gromacs 
4.07.The eigenvector.trr files that work with make_edi were generated using 
gromacs 3.3 and g_covar -fit.I can't think of any other difference between the 
.trr files I have.
In any case I am running a new g_covar with the -fit option to see if that is 
the problem.ThanksVijaya



From: ckut...@gwdg.de
Subject: Re: [gmx-users] make_edi
Date: Fri, 23 Apr 2010 10:05:12 +0200
To: gmx-users@gromacs.org



Hi Vijaya,
what version of Gromacs is this and how big do the trr fileshave to be so that 
the segv shows up?
Carsten


On Apr 22, 2010, at 6:56 PM, vijaya subramanian wrote:Hi
When I run make_edi with a small eigenvec.trr file it works, but gives me a 
segmentation fault when I input large .trr files generated using g_covar.  
These large eigenvector
files work well with g_anaeig and I have used them to generate projections as 
well as filtered trajectories.
The command line with options for make_edi is given below: 

make_edi -linfix "4,5,7,8" -outfrq 500 -f eigvec.trr -s fframe.gro  -o 
edsamp.edi -linstep ".0001 .0001 .0001 .0001"


One option would be to read the large eigenvec.trr file and write out only the 
eigenvectors
I need to a new file.  Is there some way I can do that?  Else, is there some 
way to modify
make_edi so I don't get a segmentation fault.

Thanks
Vijaya

The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with 
Hotmail. Get busy. -- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


                                          
_________________________________________________________________
The New Busy is not the old busy. Search, chat and e-mail from your inbox.
http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_3
-- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to