[gmx-users] Problem reading large file in g_covar

[Sridhar Acharya]

Hello,

I am running g_covar compiled on a sun4 architechture system running 
solaris 9.
But the program halts with the error message that the given xtc file was 
not found.
In fact the xtc file which is 7.1GB was very much existing. I suppose 
that it is a case of large file.
I  compiled GROMACS3.1.4 with --enable-largefile. But still the same 
error occurs.
How to make g_covar recognise this file?

##########################################################################
                         :-)  G  R  O  M  A  C  S  (-:

               GRoups of Organic Molecules in ACtion for Science

                            :-)  VERSION 3.1.4  (-:


       Copyright (c) 1991-2002, University of Groningen, The Netherlands
         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.

         :-)  
/users/sridhar/bin/GROMACS314_SOLARIS/SERIAL/sparc-sun-solaris2.9/ultrasparc3/bin/g_covar  
(-:

Option     Filename  Type          Description
------------------------------------------------------------
  -f    50NS_WT.xtc  Input         Generic trajectory: xtc trr trj gro 
g96 pdb
  -s ../FILES/b4md_1cyp_WT.tpr  Input         Structure+mass(db): tpr 
tpb tpa
                                   gro g96 pdb
  -n ../FILES/pr_1cyp_WT.ndx  Input, Opt!   Index file
  -o eigenval_WT.xvg  Output        xvgr/xmgr file
  -v eigenvec_WT.trr  Output        Full precision trajectory: trr trj
 -av average_WT.pdb  Output        Generic structure: gro g96 pdb
  -l   covar_WT.log  Output        Log file
-xpm      covar.xpm  Output, Opt.  X PixMap compatible matrix file
-xpma    covara.xpm  Output, Opt.  X PixMap compatible matrix file

      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
          -b   time  12000  First frame (ps) to read from trajectory
          -e   time  50000  Last frame (ps) to read from trajectory
         -dt   time     -1  Only use frame when t MOD dt = first time (ps)
         -tu   enum     ps  Time unit: ps, fs, ns, us, ms, s, m or h
    -[no]fit   bool    yes  Fit to a reference structure
    -[no]ref   bool     no  Use the deviation from the conformation in the
                            structure file instead of from the average
    -[no]mwa   bool     no  Mass-weighted covariance analysis
       -last    int     -1  Last eigenvector to write away (-1 is till the
                            last)

Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision)
Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision)

Choose a group for the least squares fit
Group     0 (      System) has 41820 elements
Group     1 (     Protein) has  4858 elements
Group     2 (   Protein-H) has  3775 elements
Group     3 (     C-alpha) has   478 elements
Group     4 (    Backbone) has  1434 elements
Group     5 (   MainChain) has  1913 elements
Group     6 (MainChain+Cb) has  2361 elements
Group     7 ( MainChain+H) has  2363 elements
Group     8 (   SideChain) has  2495 elements
Group     9 ( SideChain-H) has  1862 elements
Group    10 ( Prot-Masses) has  4858 elements
Group    11 ( Non-Protein) has 36962 elements
Group    12 (        HEME) has    47 elements
Group    13 (         SOL) has 36912 elements
Group    14 (         CL-) has     3 elements
Group    15 (       Other) has 36962 elements
Group    16 (Protein_HEME) has  4905 elements
Group    17 (Protein_HEME_CL-) has  4908 elements
Select a group: 3

Choose a group for the covariance analysis
Group     0 (      System) has 41820 elements
Group     1 (     Protein) has  4858 elements
Group     2 (   Protein-H) has  3775 elements
Group     3 (     C-alpha) has   478 elements
Group     4 (    Backbone) has  1434 elements
Group     5 (   MainChain) has  1913 elements
Group     6 (MainChain+Cb) has  2361 elements
Group     7 ( MainChain+H) has  2363 elements
Group     8 (   SideChain) has  2495 elements
Group     9 ( SideChain-H) has  1862 elements
Group    10 ( Prot-Masses) has  4858 elements
Group    11 ( Non-Protein) has 36962 elements
Group    12 (        HEME) has    47 elements
Group    13 (         SOL) has 36912 elements
Group    14 (         CL-) has     3 elements
Group    15 (       Other) has 36962 elements
Group    16 (Protein_HEME) has  4905 elements
Group    17 (Protein_HEME_CL-) has  4908 elements
Select a group: 3

Note: the fit and analysis group are identical,
      while the fit is mass weighted and the analysis is not.
      Making the fit non mass weighted.

Constructing covariance matrix (1434x1434)...
Fatal error: File 50NS_WT.xtc not found
#################################################################################

-- 
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
http://www.cdfd.org.in
email: sridhar at cdfd.org.in
sridharfirst at gmail.com
sridharacharya at indiatimes.com
Phone: Lab: +91-8413-235467*2044
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