[gmx-users] Problem reading large file in g_covar

[Sridhar Acharya]

Hello,

I am running g_covar. 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
Home: +91-40-27505833
Mobile: +91-9866147193