[gmx-users] Glibc error in Make_edi module
Guo Zhi
gzgzgz at gmail.com
Sun Oct 8 10:12:37 CEST 2006
I am trying the flooding method in gromacs package, using a 57 atom system,
Met-enkephalin.
Following the steps in J. Comp. Chem. by Oliver F.Lange et al.
The problem now I have is in Make_edi procedure:
shark at server:~/Met_enkephalin/flood/nm/back_result$ make_edi -f
eigenvec.trr-eig
eigenval.xvg -s minimized_d2.pdb -o sam.edi -flood 7-12 -tau 2 -deltaF0 3
-hesse
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, 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 eigenvec.trr Input Full precision trajectory: trr trj
-eig eigenval.xvg Input, Opt! xvgr/xmgr file
-s minimized_d2.pdb Input Structure+mass(db): tpr tpb tpa gro g96
pdb xml
-n index.ndx Input, Opt. Index file
-tar target.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-ori origin.gro Input, Opt. Generic structure: gro
g96 pdb tpr tpb tpa
xml
-o sam.edi Output ED sampling input
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-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, v
and f (e.g. 1,2-5,9) or 1-100:10 means 1 11 21
31
... 91
-linfix string Indices of eigenvectors for fixed increment
linear sampling
-linacc string Indices of eigenvectors for acceptance linear
sampling
-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
-flood string 7-12 Indices of eigenvectors for flooding
-outfrq int 100 freqency (in steps) of writing output in .edo
file
-logfrq int 100 frequency (in steps) of writing to log
-slope real 0 minimal slope in acceptance radius expamsion
-maxedsteps int 0 max nr of steps per cycle
-deltaF0 real 3 target destabilization energy - used for
flooding
-deltaF real 0 start deltaF with this parameter - default 0,
i.g. nonzero values only needed for restart
-tau real 2 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 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]hesse bool yes the eigenvectors and eigenvalues are from a
Hesse
matrix
-[no]harmonic bool no the eigenvalues are interpreted as spring
constant
list -linfix consist of the indices:
list -linacc consist of the indices:
list -flood consist of the indices:7 8 9 10 11 12
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 (double precision)
Read non mass weighted average/minimum structure with 57 atoms from
eigenvec.trr
*** glibc detected *** realloc(): invalid size: 0xafc87728 ***
Aborted
*
The minimization process give a eigenvalue like the following
# This file was created Sun Oct 8 15:44:56 2006
# by the following command:
# g_nmeig_d -f nm.mtx -ol eigenval.xvg -v eigenvec.trr -nom -s nm.tpr
#
# g_nmeig_d is part of G R O M A C S:
#
# GROwing Monsters And Cloning Shrimps
#
@ title "Eigenvalues"
@ xaxis label "Eigenvalue index"
@ yaxis label "Eigenvalue [Gromacs units]"
@TYPE xy
@ subtitle "not mass weighted"
1 -0.000154062
2 -2.6221e-05
3 -5.25179e-07
4 5.7697e-06
5 1.09519e-05
6 0.000101721
7 35.8779
8 49.6637
9 59.073
10 110.422
11 168.313
12 282.994
13 449.308
14 580.922
15 638.459
16 852.573
17 1059.74
18 1183.52
19 1418.77
20 1528.05
21 1665.92
I am not sure whether the first 6 values are small enough or not for use.
I tried other small peptides, problem still exist.
I first used cut-off. Then from previous mail-list, I knowed that some bugs
exist in 3.3.1, so I changed it to PME, problem still exist.
I am sure whether it depends on certain platform or linux kernel, I have not
ever tried other platform.
Any advice is appreciated
--
Guo Zhi
Department of Physics, Fudan University
Computational Biophysics Group
Address: No. 220 Handan Rd., Shanghai
Zip code: 200433
Phone: 80-021-65643521
mail: gzgzgz at gmail.com OR 042019028 at fudan.edu.cn
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