[gmx-users] Gromacs error
Dear GROMACS Developers and users, While trying to clustering analysis based on certain distance matrices, however, while trying to perform PCA, I executed the following command, it shows the following error. Need your valuable suggestion and feedback to get rid of such errors. Thanking you Budheswar gmx covar -f pca.xtc -s pca_dummy.pdb -nofit -nomwa -nopbc :-) GROMACS - gmx covar, 2019.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca HamuraruVincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. LemkulViveca LindahlMagnus Lundborg Erik Marklund Pascal Merz Pieter MeulenhoffTeemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael ShirtsAlexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian WennbergMaarten 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) 2001-2018, 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 covar, version 2019.2 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/bd422/Desktop/BD/1 Command line: gmx covar -f pca.xtc -s pca_dummy.pdb -nofit -nomwa -nopbc WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Choose a group for the covariance analysis Group 0 ( System) has 66506 elements Group 1 (Protein) has 66506 elements Group 2 ( Protein-H) has 66506 elements Group 3 (C-alpha) has 66506 elements Group 4 ( Backbone) has 66506 elements Group 5 ( MainChain) has 66506 elements Group 6 ( MainChain+Cb) has 66506 elements Group 7 (MainChain+H) has 66506 elements Group 8 ( SideChain) has 0 elements Group 9 (SideChain-H) has 0 elements Select a group: 0 Selected 0: 'System' --- Program: gmx covar, version 2019.2 Source file: src/gromacs/utility/smalloc.cpp (line 125) Fatal error: Not enough memory. Failed to calloc 39807432324 elements of size 4 for mat (called from file /home/bd422/Downloads/gromacs-2019.2/src/gromacs/gmxana/gmx_covar.cpp, line 260) 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? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Help needed in using gmx select
Dear Gromacs Developers and Users, I need a small help in GROMACS trajectory analysis. I want to define a selection i.e., 4Ang volume around two residues (from different chains X and chain Y ) that make your binding site --- Within this selection I want count number of waters molecules along the trajectory (it's a lipid bilayer system with TIP3P and POPC). How can I estimate the number of water molecules using gmx select and gmx dist or gmx mindist..through gromacs or VMD. Looking forward to hear from you Thanking You Sincere Regards Budheswar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Help needed using gmx select of GROMACS
Dear Gromacs Developers and Users, I need a small help in GROMACS trajectory analysis. I want to define a selection i.e., 4Ang volume around two residues (from different chains X and chain Y ) that make your binding site --- Within this selection I want count number of waters molecules along the trajectory (it's a lipid bilayer system with TIP3P and POPC). How can I estimate the number of water molecules using gmx select and gmx dist or gmx mindist..through gromacs or VMD. Looking forward to hear from you Thanking You Sincere Regards Budheswar [http://www.dtu.dk/-/media/DTU_Generelt/Andet/mail-signature-logo.png] Budheswar Dehury Postdoc b...@kemi.dtu.dk<mailto:b...@kemi.dtu.dk> Kemitorvet Building 206 2800 Kgs. Lyngby www.dtu.dk/english<https://www.dtu.dk/english> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GMX TRJCONV ERROR and GMX CHECK ERROR
Dear All, Can anybody suggest what should be ideal solution for this the blow mentioned two errors using gmx trjconv and gmx check error in GROMACS 2018.4 GROMACS: gmx trjconv, version 2018.3-dev-20181031-cfa1b1c Executable: /apps/gromacs/gromacs-2018.4-git/bin/gmx Data prefix: /apps/gromacs/gromacs-2018.4-git Working dir: /run/media/bude/Data/BD/S_OPEN/SOpen/WILDTYPE/Seed3 Command line: gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md.xtc -pbc mol -ur compact Will write xtc: Compressed trajectory (portable xdr format): xtc Reading file md_0_1.tpr, VERSION 2018.2 (single precision) Reading file md_0_1.tpr, VERSION 2018.2 (single precision) --- Program: gmx trjconv, version 2018.3-dev-20181031-cfa1b1c Source file: src/gromacs/topology/symtab.cpp (line 137) Fatal error: symtab get_symtab_handle 21279775 not found and GROMACS: gmx check, version 2018.3-dev-20181031-cfa1b1c Executable: /apps/gromacs/gromacs-2018.4-git/bin/gmx Data prefix: /apps/gromacs/gromacs-2018.4-git Working dir: /run/media/bude/Data/BD/S_OPEN/SOpen/WILDTYPE/Seed3 Command line: gmx check -f md_0_1.xtc Checking file md_0_1.xtc Reading frame 0 time0.000 # Atoms 235013 Precision 0.001 (nm) Reading frame 1 time 20.000 Warning at frame 1: there are 17527 particles with all coordinates zero --- Program: gmx check, version 2018.3-dev-20181031-cfa1b1c Source file: src/gromacs/fileio/xtcio.cpp (line 91) Fatal error: Magic Number Error in XTC file (read 0, should be 1995) The log file displays log statistics without any error while I tried to analyze it says the following errors. I need your valuable suggestion and guidance. Thanking You With Warm Regards Budheswar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Error: GROMACS GMX HLEIX segmentation Fault
Dear Gromacs Develeopment Team, Hello...I have the same segmentation fault of gmx helix even after updating with the revised version and/or applying the patch for the same. further I have alos tried to compile using the source-code of the latest version, I am facing the same segmentation fault problem. Here is the command that I executed ..and the error GROMACS: gmx helix, version 2019-beta2-dev-20181026-7ce2d66 Executable: /apps/gromacs/gromacs-2019-git/bin/gmx Data prefix: /apps/gromacs/gromacs-2019-git Working dir: /run/media/bude//Helix/TM1 Command line: gmx helix -s ../md.tpr -f ../md.xtc -n index.ndx Reading file ../md.tpr, VERSION 2018.2 (single precision) Reading frame 0 time 20.000 Please select a group containing the entire backbone Group 0 ( System) has 201382 elements Group 1 (Protein) has 22327 elements Group 2 ( Protein-H) has 11159 elements Group 3 (C-alpha) has 1414 elements Group 4 ( Backbone) has 4242 elements Group 5 ( MainChain) has 5651 elements Group 6 ( MainChain+Cb) has 6978 elements Group 7 (MainChain+H) has 6986 elements Group 8 ( SideChain) has 15341 elements Group 9 (SideChain-H) has 5508 elements Group10 (Prot-Masses) has 22327 elements Group11 (non-Protein) has 179055 elements Group12 ( Other) has 179055 elements Group13 ( POPC) has 40468 elements Group14 ( TIP3) has 138315 elements Group15 (SOD) has 146 elements Group16 (CLA) has 126 elements Group17 (TM1) has 397 elements Select a group: 17 Selected 17: 'TM1' Checking group TM1 There are 25 residues There are 23 complete backbone residues (from 2 to 24) nall=397 Reading file ../md.tpr, VERSION 2018.2 (single precision) helix from: 8 through 23 t=20.00Segmentation fault Need your valuable input to rectify the error. Thanking You With Warm Regards Budheswar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Error in writing trajectory files using HPC (vGromacs 2018.2)
00039000 08:05 516184 /usr/lib64/libhwloc.so.5.6.8 7f76c3f25000-7f76c3f26000 r--p 00038000 08:05 516184 /usr/lib64/libhwloc.so.5.6.8 7f76c3f26000-7f76c3f27000 rw-p 00039000 08:05 516184 /usr/lib64/libhwloc.so.5.6.8 7f76c3f27000-7f76c40ea000 r-xp 08:05 515110 /usr/lib64/libc-2.17.so 7f76c40ea000-7f76c42e9000 ---p 001c3000 08:05 515110 /usr/lib64/libc-2.17.so 7f76c42e9000-7f76c42ed000 r--p 001c2000 08:05 515110 /usr/lib64/libc-2.17.so 7f76c42ed000-7f76c42ef000 rw-p 001c6000 08:05 515110 /usr/lib64/libc-2.17.so 7f76c42ef000-7f76c42f4000 rw-p 00:00 0 7f76c42f4000-7f76c430b000 r-xp 08:05 515136 /usr/lib64/libpthread-2.17.so 7f76c430b000-7f76c450a000 ---p 00017000 08:05 515136 /usr/lib64/libpthread-2.17.so 7f76c450a000-7f76c450b000 r--p 00016000 08:05 515136 /usr/lib64/libpthread-2.17.so 7f76c450b000-7f76c450c000 rw-p 00017000 08:05 515136 /usr/lib64/libpthread-2.17.so 7f76c450c000-7f76c451 rw-p 00:00 0 7f76c451-7f76c4526000 r-xp 00:bb 64558120 /appl/gcc/7.3.0/lib64/libgcc_s.so.1 7f76c4526000-7f76c4725000 ---p 00016000 00:bb 64558120 /appl/gcc/7.3.0/lib64/libgcc_s.so.1 7f76c4725000-7f76c4726000 rw-p 00015000 00:bb 64558120 /appl/gcc/7.3.0/lib64/libgcc_s.so.1 7f76c4726000-7f76c4753000 r-xp 00:bb 64559071 /appl/gcc/7.3.0/lib64/libgomp.so.1.0.0 7f76c4753000-7f76c4952000 ---p 0002d000 00:bb 64559071 /appl/gcc/7.3.0/lib64/libgomp.so.1.0.0 7f76c4952000-7f76c4953000 rw-p 0002c000 00:bb 64559071 /appl/gcc/7.3.0/lib64/libgomp.so.1.0.0 7f76c4953000-7f76c4a54000 r-xp 08:05 515118 /usr/lib64/libm-2.17.so 7f76c4a54000-7f76c4c53000 ---p 00101000 08:05 515118 /usr/lib64/libm-2.17.so 7f76c4c53000-7f76c4c54000 r--p 0010 08:05 515118 /usr/lib64/libm-2.17.so 7f76c4c54000-7f76c4c55000 rw-p 00101000 08:05 515118 /usr/lib64/libm-2.17.so 7f76c4c55000-7f76c4ddd000 r-xp 00:bb 64558932 /appl/gcc/7.3.0/lib64/libstdc++.so.6.0.24 7f76c4ddd000-7f76c4fdc000 ---p 00188000 00:bb 64558932 /appl/gcc/7.3.0/lib64/libstdc++.so.6.0.24 7f76c4fdc000-7f76c4fe6000 r--p 00187000 00:bb 64558932 /appl/gcc/7.3.0/lib64/libstdc++.so.6.0.24 7f76c4fe6000-7f76c4fe8000 rw-p 00191000 00:bb 64558932 /appl/gcc/7.3.0/lib64/libstdc++.so.6.0.24 7f76c4fe8000-7f76c4fec000 rw-p 00:00 0 7f76c4fec000-7f76c6226000 r-xp 00:bb 70350216 /appl/gromacs/2018.2/XeonE5-2680v2/lib64/libgromacs.so.3.2.0 7f76c6226000-7f76c6425000 ---p 0123a000 00:bb 70350216 /appl/gromacs/2018.2/XeonE5-2680v2/lib64/libgromacs.so.3.2.0 7f76c6425000-7f76c6434000 r--p 01239000 00:bb 70350216 /appl/gromacs/2018.2/XeonE5-2680v2/lib64/libgromacs.so.3.2.0 7f76c6434000-7f76c6455000 rw-p 01248000 00:bb 70350216 /appl/gromacs/2018.2/XeonE5-2680v2/lib64/libgromacs.so.3.2.0 7f76c6455000-7f76c6458000 rw-p 00:00 0 7f76c6458000-7f76c647a000 r-xp 08:05 517714 /usr/lib64/ld-2.17.so 7f76c6647000-7f76c6651000 rw-p 00:00 0 7f76c6676000-7f76c6679000 rw-p 00:00 0 7f76c6679000-7f76c667a000 r--p 00021000 08:05 517714 /usr/lib64/ld-2.17.so 7f76c667a000-7f76c667b000 rw-p 00022000 08:05 517714 /usr/lib64/ld-2.17.so 7f76c667b000-7f76c667c000 rw-p 00:00 0 7ffe11b1d000-7ffe11b3f000 rw-p 00:00 0 [stack] 7ffe11be3000-7ffe11be5000 r-xp 00:00 0 [vdso] ff60-ff601000 r-xp 00:00 0 [vsyscall] Aborted /work3/bude/PS2_G_Secretase/Seed1/Helix Furthermore, most important thing is that the gmx helix command doesn't work in GROMACS2018.2 version, its showing the segmentation fault..I am unsure about the error...Please help me it fix these error...While I analyzed other helix properties like gmx helixorient, gmx bundle..they are working fine... Further while defining the Helix in the index should we use atom or amino acid In case of analysis -ahxstart and -ahxend option what should be the integer (either amino acid number of the first and last position or something else) Anticipating for a positive reply from your end. Thanking You With Warm Regards Budheswar Dehury Post-Doctoral Fellow DTU, Chemistry, Denmark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https
[gmx-users] GMX Helix Segmentation fault
Dear All, Hello. I am doing analysis soem analysis of TM helix properties using the GMX helix tool of GROMACS 2018.2. Though, in someways its working in the old version 2016.2 but its not working in the latest 2018.2 version. I have appended the following error. gmx helix -f ../md.xtc -s ../md.tpr -n index.ndx Reading file ../md.tpr, VERSION 2018.2 (single precision) Reading frame 0 time 20.000 Please select a group containing the entire backbone Group 0 ( System) has 201382 elements Group 1 (Protein) has 22327 elements Group 2 ( Protein-H) has 11159 elements Group 3 (C-alpha) has 1414 elements Group 4 ( Backbone) has 4242 elements Group 5 ( MainChain) has 5651 elements Group 6 ( MainChain+Cb) has 6978 elements Group 7 (MainChain+H) has 6986 elements Group 8 ( SideChain) has 15341 elements Group 9 (SideChain-H) has 5508 elements Group10 (Prot-Masses) has 22327 elements Group11 (non-Protein) has 179055 elements Group12 ( Other) has 179055 elements Group13 ( POPC) has 40468 elements Group14 ( TIP3) has 138315 elements Group15 (SOD) has 146 elements Group16 (CLA) has 126 elements Group17 ( a_10743-11091) has 349 elements Select a group: 17 Selected 17: 'a_10743-11091' Checking group a_10743-11091 There are 21 residues There are 19 complete backbone residues (from 2 to 20) nall=349 Reading file ../md.tpr, VERSION 2018.2 (single precision) Please help me to rectify this error or suggest any idea how should I get reed of this. Thanking you With Warm Regards Budheswar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
