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";<272699...@qq.com>; Date: Mon, Aug 14, 2017 00:25 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@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";<272699...@qq.com>; Date: Mon, Aug 14, 2017 00:09 AM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@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";<272699...@qq.com>; Date: Sun, Aug 13, 2017 10:52 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@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 ------------------------------------------------------- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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