[gmx-users] make_edi

vijaya subramanian vijaya65 at hotmail.com
Fri Apr 23 17:43:21 CEST 2010

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: ckutzne at gwdg.de
Subject: Re: [gmx-users] make_edi
Date: Fri, 23 Apr 2010 10:05:12 +0200
To: gmx-users at 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?

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.


The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. Get busy. -- 
gmx-users mailing list    gmx-users at gromacs.org
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

The New Busy is not the old busy. Search, chat and e-mail from your inbox.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100423/8f2c550a/attachment.html>

More information about the gromacs.org_gmx-users mailing list