[gmx-users] make_edi, g_covar -nofit

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 5 02:08:03 CEST 2010


On 5/05/2010 6:56 AM, vijaya subramanian wrote:
> Hi Carsten
> A couple of quick questions:
> I already have gromacs-4.0.7 downloaded from the gromacs website. I
> found that I couldn't
> use git checkout --track -b release-4-0-patches
> origin/release-4-0-patches to get the patches.
> fatal: Not a git repository
> Do I have to uninstall gromacs-4.0.7 and re-install gromacs obtained
> from the git site as below,
> then install gromacs again?

No. Leave your normal installation alone. Download the git repository 
according to the instructions on the webpage (the stuff below looks ok). 
bootstrap, configure and compile it. Then either run 
git-gromacs/src/tools/make_edi by hand, or copy it to your installation 
directory in place of the 4.0.7 make_edi.

Mark

> git clone git://git.gromacs.org/gromacs.git
> git checkout --track -b release-4-0-patches origin/release-4-0-patches
>
> Thanks
> vijaya
>
> ------------------------------------------------------------------------
> From: ckutzne at gwdg.de
> Subject: Re: [gmx-users] make_edi, g_covar -nofit
> Date: Tue, 4 May 2010 18:04:17 +0200
> To: gmx-users at gromacs.org
>
> 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 <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: ckutzne at gwdg.de <mailto: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 <mailto:gmx-users at gromacs.org>
>
>     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
>
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> --
> 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
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