[gmx-users] make_edi fails with multiple eigenvectors for -linfix and -linacc
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Wed Dec 23 21:06:50 CET 2009
Hello,
I am having trouble getting make_edi -linfix to work with multiple
eigenvectors.
This works for a single EV:
$ echo 3 | make_edi -s ../../SETUP/makeTPR/edi.tpr -f
../../SETUP/makeEDI/eigenvec.trr -o testpositive.edi -linfix "1"
-linstep "0.0001" -outfrq 50
And throws an error for:
$ echo 3 | make_edi -s ../../SETUP/makeTPR/edi.tpr -f
../../SETUP/makeEDI/eigenvec.trr -o testpositive.edi -linfix "1 2"
-linstep "0.0001 0.0001" -outfrq 50
"Error in the list of eigenvectors for -linfix at pos 2 with char"
Here is the output, first for the error, then for the single EV that
works, then showing that I get the same error with -linacc
I included quotes around the -linfix list and ran it directly from the
command line (no script) to be entirely sure that the quotes were
being passed to gromacs and not interpreted by the shell. In any
event, without the quotes it is not interpreted as a string and
complains about the unknown argument "2".
There is an old mailing list post that suggests my intnded usage is
expected to work:
http://lists.gromacs.org/pipermail/gmx-users/2005-August/016638.html
Is the WHATIF software still 100% compatible with gromacs? I suppose
that I could just skip make_edi all together in favour of WHATIF if
the problem here is not in my usage and is not easily repaired.
Thank you,
Chris.
$ echo 3 | make_edi -s ../../SETUP/makeTPR/edi.tpr -f
../../SETUP/makeEDI/eigenvec.trr -o testpositive.edi -linfix "1 2"
-linstep "0.0001 0.0001" -outfrq 50
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) VERSION 4.0.5 (-:
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 ../../SETUP/makeEDI/eigenvec.trr Input Full precision
trajectory: trr trj cpt
-eig eigenval.xvg Input, Opt. xvgr/xmgr file
-s ../../SETUP/makeTPR/edi.tpr 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 testpositive.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 1 2 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 50 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 0.0001 0.0001 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
-------------------------------------------------------
Program make_edi, VERSION 4.0.5
Source code file: make_edi.c, line: 232
Fatal error:
Error in the list of eigenvectors for -linfix at pos 2 with char
-------------------------------------------------------
"It Was My Pleasure" (Pulp Fiction)
######################################
######################################
######################################
$ echo 3 | make_edi -s ../../SETUP/makeTPR/edi.tpr -f
../../SETUP/makeEDI/eigenvec.trr -o testpositive.edi -linfix "1"
-linstep "0.0001" -outfrq 50
gpc-f103n084-$ cat z
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) VERSION 4.0.5 (-:
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 ../../SETUP/makeEDI/eigenvec.trr Input Full precision
trajectory: trr trj cpt
-eig eigenval.xvg Input, Opt. xvgr/xmgr file
-s ../../SETUP/makeTPR/edi.tpr 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 testpositive.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 1 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 50 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 0.0001 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
trn version: GMX_trn_file (single precision)
Read non mass weighted reference structure with 1705 atoms from
../../SETUP/makeEDI/eigenvec.trr
Read non mass weighted average/minimum structure with 1705 atoms from
../../SETUP/makeEDI/eigenvec.trr
Read 767 eigenvectors (for 1705 atoms)
Reading file ../../SETUP/makeTPR/edi.tpr, VERSION 4.0.5 (single precision)
Reading file ../../SETUP/makeTPR/edi.tpr, VERSION 4.0.5 (single precision)
Opening library file
/scratch/cneale/GPC/exe/intel/gromacs-4.0.5/exec/share/gromacs/top/aminoacids.dat
Group 0 ( System) has 251571 elements
Group 1 ( Protein) has 28635 elements
Group 2 ( Protein-H) has 14195 elements
Group 3 ( C-alpha) has 1705 elements
Group 4 ( Backbone) has 5115 elements
Group 5 ( MainChain) has 6820 elements
Group 6 (MainChain+Cb) has 8465 elements
Group 7 ( MainChain+H) has 8460 elements
Group 8 ( SideChain) has 20175 elements
Group 9 ( SideChain-H) has 7370 elements
Group 10 ( Prot-Masses) has 28635 elements
Group 11 ( Non-Protein) has 222936 elements
Group 12 ( DMPC) has 24564 elements
Group 13 ( NA+) has 45 elements
Group 14 ( SOL) has 198327 elements
Group 15 ( Other) has 222936 elements
Select a group:
-------------------------------------------------------
Program make_edi, VERSION 4.0.5
Source code file: index.c, line: 669
Fatal error:
Cannot read from input
-------------------------------------------------------
"Right Now My Job is Eating These Doughnuts" (Bodycount)
list -linfix consist of the indices:1
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:
Select an index group of 1705 elements that corresponds to the eigenvectors
Selected 3: 'C-alpha'
################################
################################
################################
And I get the same error when I use linacc in place of linfix
echo 3 | make_edi -s ../../SETUP/makeTPR/edi.tpr -f
../../SETUP/makeEDI/eigenvec.trr -o testpositive.edi -linacc "1 2"
-accdir "0.0001 0.0001" -outfrq 50
...
Program make_edi, VERSION 4.0.5
Source code file: make_edi.c, line: 232
Fatal error:
Error in the list of eigenvectors for -linacc at pos 2 with char
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