[gmx-users] Magic Number Error in XTC file (read 0, should be 1995)
ZHANG Cheng
272699575 at qq.com
Sun Aug 13 18:47:39 CEST 2017
Hi Justin,
Thank you for explaining that.
You said "a more reliable system", what does this mean? It is my first time adding glycines to my protein using OPLS-AA/L force field. Do you think this might be the reason, and should I switch to another force field?
My procedure is as follows:
1) I get the glycine and protein pdb, convert them to .gro files using
gmx pdb2gmx -f glycine/protein.pdb -o glycine/protein.gro -water spce -inter
2) then I add the protein.gro into a box, get the protein_newbox.gro:
gmx editconf -f protein.gro -o protein_newbox.gro -c -d 1.0 -bt cubic
3) then I add glycines to this box:
gmx insert-molecules -ci glycine.gro -nmol 203 -f protein_newbox.gro -o protein_203_glycine.gro
4) then I do the exactly the same thing according to your tutorial, i.e. solvent with water, add ions, energy minimization, NVT, NPT, and finally the MD.
Can I ask if the procedure is correct? Would you please recommend some tutorial for prepare a system with protein and excipients (e.g. glycine, sorbitol, etc)?
Thank you.
------------------ Original ------------------
From: "ZHANG Cheng";<272699575 at qq.com>;
Date: Mon, Aug 14, 2017 00:25 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
Subject: Re:Re: Magic Number Error in XTC file (read 0, should be 1995)
Hi Justin,
Thank you. But how can I know where it goes wrong, and how can I avoid that?
If the trajectory is corrupt, why this 40 ns MD can still be continued to longer MD?
Why it is okay in the beginning, but becomes corrupt later?
My MD is a protein with 203 glycines in a 10x10x10 ns box filled with water and NaCl.
------------------ Original ------------------
From: "ZHANG Cheng";<272699575 at qq.com>;
Date: Mon, Aug 14, 2017 00:09 AM
To: "ZHANG Cheng"<272699575 at qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
Subject: Re: Magic Number Error in XTC file (read 0, should be 1995)
I also run "gmx check" to examine what is wrong:
gmx check -s1 md_0_1.tpr -f md_0_1.xtc
However, the same thing happened:
Command line:
gmx check -s1 md_0_1.tpr -f md_0_1.xtc
Reading file md_0_1.tpr, VERSION 5.1.1 (single precision)
Reading frame 0 time 0.000
# Atoms 127073
Precision 0.001 (nm)
Reading frame 1 time 10.000
Reading frame 2 time 20.000
Reading frame 3 time 30.000
Reading frame 4 time 40.000
Reading frame 5 time 50.000
Reading frame 6 time 60.000
Reading frame 7 time 70.000
Reading frame 8 time 80.000
Reading frame 9 time 90.000
Reading frame 10 time 100.000
Reading frame 11 time 110.000
Reading frame 12 time 120.000
-------------------------------------------------------
Program gmx check, 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
-------------------------------------------------------
------------------ Original ------------------
From: "ZHANG Cheng";<272699575 at qq.com>;
Date: Sun, Aug 13, 2017 10:52 PM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
Cc: "ZHANG Cheng"<272699575 at qq.com>;
Subject: Magic Number Error in XTC file (read 0, should be 1995)
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
-------------------------------------------------------
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