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