Hi Vijaya, please check out the newest 4.0 version from the git release-4-0-patches branch. The make_edi problem should be fixed there.
Regards, Carsten On Apr 26, 2010, at 11:19 PM, vijaya subramanian wrote: > Hi > I checked again with Gromacs 4.0.7 and I find that I have a problem > with make_edi when I use eigenvec.trr files generated using g_covar > -nofit. I use the -nofit option because the data was already fit to a > reference structure > using trjconv -fit rot+trans. > I end up with a segmentation fault when I use the following command: > > make_edi -linfix "4,5,7,8" -outfrq 500 -f evec170nfit.trr -s > fframe170compact.gro -o edsamp.edi -linstep ".000001 .000001 .000001 .000001" > > As before I get the following message: > > :-) G R O M A C S (-: > > Good ROcking Metal Altar for Chronical Sinners > > :-) VERSION 4.0.7 (-: > > > Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2008, The GROMACS development team, > check out http://www.gromacs.org for more information. > > This program is free software; you can redistribute it and/or > modify it under the terms of the GNU General Public License > as published by the Free Software Foundation; either version 2 > of the License, or (at your option) any later version. > > :-) make_edi (-: > > Option Filename Type Description > ------------------------------------------------------------ > -f evec170nfit.trr Input Full precision trajectory: trr trj cpt > -eig eigenval.xvg Input, Opt. xvgr/xmgr file > -s fframe170compact.gro Input Structure+mass(db): tpr tpb tpa gro > g96 pdb > -n index.ndx Input, Opt. Index file > -tar target.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -ori origin.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -o edsamp.edi Output ED sampling input > > Option Type Value Description > ------------------------------------------------------ > -[no]h bool no Print help info and quit > -nice int 0 Set the nicelevel > -[no]xvgr bool yes Add specific codes (legends etc.) in the output > xvg files for the xmgrace program > -mon string Indices of eigenvectors for projections of x > (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91 > -linfix string 4,5,7,8 Indices of eigenvectors for fixed increment > linear sampling > -linacc string Indices of eigenvectors for acceptance linear > sampling > -flood string Indices of eigenvectors for flooding > -radfix string Indices of eigenvectors for fixed increment > radius expansion > -radacc string Indices of eigenvectors for acceptance radius > expansion > -radcon string Indices of eigenvectors for acceptance radius > contraction > -outfrq int 500 Freqency (in steps) of writing output in .edo file > -slope real 0 Minimal slope in acceptance radius expansion > -maxedsteps int 0 Max nr of steps per cycle > -deltaF0 real 150 Target destabilization energy - used for flooding > -deltaF real 0 Start deltaF with this parameter - default 0, > i.e. nonzero values only needed for restart > -tau real 0.1 Coupling constant for adaption of flooding > strength according to deltaF0, 0 = infinity i.e. > constant flooding strength > -eqsteps int 0 Number of steps to run without any perturbations > -Eflnull real 0 This is the starting value of the flooding > strength. The flooding strength is updated > according to the adaptive flooding scheme. To use > a constant flooding strength use -tau 0. > -T real 300 T is temperature, the value is needed if you want > to do flooding > -alpha real 1 Scale width of gaussian flooding potential with > alpha^2 > -linstep string .000001 .000001 .000001 .000001 Stepsizes (nm/step) for > fixed increment linear sampling (put in quotes! > "1.0 2.3 5.1 -3.1") > -accdir string Directions for acceptance linear sampling - only > sign counts! (put in quotes! "-1 +1 -1.1") > -radstep real 0 Stepsize (nm/step) for fixed increment radius > expansion > -[no]restrain bool no Use the flooding potential with inverted sign -> > effects as quasiharmonic restraining potential > -[no]hessian bool no The eigenvectors and eigenvalues are from a > Hessian matrix > -[no]harmonic bool no The eigenvalues are interpreted as spring constant > > list -linfix consist of the indices:4 5 7 8 > list -linacc consist of the indices: > list -flood consist of the indices: > list -radfix consist of the indices: > list -radacc consist of the indices: > list -radcon consist of the indices: > list -mon consist of the indices: > trn version: GMX_trn_file (single precision) > Eigenvectors in evec170nfit.trr were determined without fitting > Read non mass weighted average/minimum structure with 4128 atoms from > evec170nfit.trr > Read 2000 eigenvectors (for 4128 atoms) > > > Select an index group of 4128 elements that corresponds to the eigenvectors > Opening library file > /sw/analysis/gromacs/4.0.7/centos5.4_pgi8.0.4/share/gromacs/top/aminoacids.dat > Group 0 ( System) has 4128 elements > Group 1 ( Protein) has 4128 elements > Group 2 ( Protein-H) has 4128 elements > Group 3 ( C-alpha) has 4128 elements > Group 4 ( Backbone) has 4128 elements > Group 5 ( MainChain) has 4128 elements > Group 6 (MainChain+Cb) has 4128 elements > Group 7 ( MainChain+H) has 4128 elements > Group 8 ( SideChain) has 0 elements > Group 9 ( SideChain-H) has 0 elements > Select a group: 3 > Selected 3: 'C-alpha' > > Segmentation fault > > With the eigenvector.trr generated using g_covar -fit option I don't get the > segmentation fault. The following line in the above log file > " Eigenvectors in evec170nfit.trr were determined without fitting" is > replaced instead > with > "Read non mass weighted reference structure with 4128 atoms from > evec170fit.trr" > and I get the edsamp.edi file. > > I already performed covariance analyses using the -nofit option on my large > protein and would like to use the results I have so far if possible. If > anyone knows > what the problem is, it would be of great help. > > Thanks > Vijaya > > From: [email protected] > Subject: Re: [gmx-users] make_edi > Date: Fri, 23 Apr 2010 10:05:12 +0200 > To: [email protected] > > Hi Vijaya, > > what version of Gromacs is this and how big do the trr files > have 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > Hotmail is redefining busy with tools for the New Busy. Get more from your > inbox. See how. -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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