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: [email protected]
Subject: Re: [gmx-users] make_edi, g_covar -nofit
Date: Tue, 4 May 2010 18:04:17 +0200
To: [email protected]
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: [email protected] <mailto:[email protected]>
Subject: Re: [gmx-users] make_edi
Date: Fri, 23 Apr 2010 10:05:12 +0200
To: [email protected] <mailto:[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
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Theoretical and Computational Biophysics
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