[gmx-users] Magic Number Error in XTC file (read 0, should be 1995)

[ZHANG Cheng]

Dear Gromacs,
I am trying to analyse my xtc file (40 ns) using:
echo 0|gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact


However, it shows:
...
Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)

...


Then I re-run the MD from the start from a same tpr file for 0.39 ns and run the "trjconv", and it works all fine.


So I think, maybe the 40 ns xtc file has something wrong during the MD. But the 40 ns MD could still be continued from a cpt file, so I am not sure where it actually goes wrong.


Thank you.


Yours sincerely
Cheng


------------------------------------------------
The whole log for "trjconv" of the 40 ns MD:


                  :-) GROMACS - gmx trjconv, VERSION 5.1.1 (-:


                            GROMACS is written by:
     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra   Sebastian Fritsch 
  Gerrit Groenhof   Christoph Junghans   Anca Hamuraru    Vincent Hindriksen
 Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten Kutzner  
    Per Larsson      Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff 
   Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk   
   Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers  
   Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel


Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.


GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.


GROMACS:      gmx trjconv, VERSION 5.1.1
Executable:   /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2/bin//gmx
Data prefix:  /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2
Command line:
  gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact


Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file md_0_1.tpr, VERSION 5.1.1 (single precision)
Reading file md_0_1.tpr, VERSION 5.1.1 (single precision)
Group     0 (         System) has 127073 elements
Group     1 (        Protein) has  8850 elements
Group     2 (      Protein-H) has  4351 elements
Group     3 (        C-alpha) has   645 elements
Group     4 (       Backbone) has  1935 elements
Group     5 (      MainChain) has  2785 elements
Group     6 (   MainChain+Cb) has  3194 elements
Group     7 (    MainChain+H) has  3816 elements
Group     8 (      SideChain) has  5034 elements
Group     9 (    SideChain-H) has  1566 elements
Group    10 (    Prot-Masses) has  8850 elements
Group    11 (    non-Protein) has 118223 elements
Group    12 (          Water) has 117684 elements
Group    13 (            SOL) has 117684 elements
Group    14 (      non-Water) has  9389 elements
Group    15 (            Ion) has   539 elements
Group    16 (             NA) has   155 elements
Group    17 (             CL) has   384 elements
Group    18 ( Water_and_ions) has 118223 elements
Select a group: 
Reading frame       0 time    0.000   
Precision of md_0_1.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
 ->  frame      0 time    0.000      


Reading frame       1 time   10.000    ->  frame      1 time   10.000      


Reading frame       2 time   20.000    ->  frame      2 time   20.000      


Reading frame       3 time   30.000    ->  frame      3 time   30.000      


Reading frame       4 time   40.000    ->  frame      4 time   40.000      


Reading frame       5 time   50.000    ->  frame      5 time   50.000      


Reading frame       6 time   60.000    ->  frame      6 time   60.000      


Reading frame       7 time   70.000    ->  frame      7 time   70.000      


Reading frame       8 time   80.000    ->  frame      8 time   80.000      


Reading frame       9 time   90.000    ->  frame      9 time   90.000      


Reading frame      10 time  100.000    ->  frame     10 time  100.000      


Reading frame      11 time  110.000   
Reading frame      12 time  120.000   
-------------------------------------------------------
Program gmx trjconv, VERSION 5.1.1
Source code file: /dev/shm/tmp.PwtfSrm0uJ/gromacs-5.1.1/src/gromacs/fileio/xtcio.c, line: 90


Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------