[gmx-users] make_edi, more info
vijaya subramanian
vijaya65 at hotmail.com
Thu Apr 22 20:43:48 CEST 2010
Hi
I have included the output from two make_edi submissions, the first one gave
a segmentation fault and the second did not. The only difference between the two is the input .trr file.
:-) make_edi (-:
Option Filename Type Description
------------------------------------------------------------
-f evec11-129.trr Input Full precision trajectory: trr trj cpt
-eig eigenval.xvg Input, Opt. xvgr/xmgr file
-s fframe4-1250ps.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 5000 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 .0001 .0001 .0001 .0001 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 evec11-129.trr were determined without fitting
Read non mass weighted average/minimum structure with 4128 atoms from evec11-129.trr
Read 12384 eigenvectors (for 4128 atoms)
Select an index group of 4128 elements that corresponds to the eigenvectors
Opening library file /usr/local/gromacs/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'
Back Off! I just backed up edsamp.edi to ./#edsamp.edi.12#
Segmentation fault
:-) make_edi (-:
Option Filename Type Description
------------------------------------------------------------
-f ev15-25.trr Input Full precision trajectory: trr trj cpt
-eig eigenval.xvg Input, Opt. xvgr/xmgr file
-s fframe4-1250ps.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 5000 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 .0001 .0001 .0001 .0001 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)
Read non mass weighted reference structure with 4128 atoms from ev15-25.trr
Read non mass weighted average/minimum structure with 4128 atoms from ev15-25.trr
Read 11600 eigenvectors (for 4128 atoms)
Select an index group of 4128 elements that corresponds to the eigenvectors
Opening library file /usr/local/gromacs/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'
Back Off! I just backed up edsamp.edi to ./#edsamp.edi.11#
gcq#178: "Ramones For Ever" (P.J. Van Maaren)
Thanks
Vijaya
From: vijaya65 at hotmail.com
To: gmx-users at gromacs.org
Date: Thu, 22 Apr 2010 16:56:32 +0000
Subject: [gmx-users] make_edi
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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