[gmx-users] make_edi, g_covar -nofit
Carsten Kutzner
ckutzne at gwdg.de
Tue May 4 18:04:17 CEST 2010
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: 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 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 gmx-users at 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-request at gromacs.org.
> 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 gmx-users at 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-request at gromacs.org.
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100504/f0c20595/attachment.html>
More information about the gromacs.org_gmx-users
mailing list