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
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.
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