[gmx-users] GRomacs 3.3.1 parallel run
Good morning, I started using Gromacs only few months ago doing MD on proteins in membranes. I' m using GRomacs 3.3.1 in parallel but I have some problems. I'm doing my simulations on a 70 nodes cluster using 4 nodes (16 processors). the system uses PBS torque and SCALIMPI libraries. When I run my jobs, the jobs start with no problems, even if there is the following error message : Jul 30 15:56:05: ([EMAIL PROTECTED])(2688) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(2690) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(4367) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(4370) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(4369) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(4368) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(2687) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(2689) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(698) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(32587) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(696) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(32584) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(32585) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(32586) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(695) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(697) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory NNODES=16, MYRANK=9, HOSTNAME=avogadro-61.n16.chimica.unipd.it NNODES=16, MYRANK=11, HOSTNAME=avogadro-61.n16.chimica.unipd.it NNODES=16, MYRANK=8, HOSTNAME=avogadro-61.n16.chimica.unipd.it NNODES=16, MYRANK=10, HOSTNAME=avogadro-61.n16.chimica.unipd.it NNODES=16, MYRANK=7, HOSTNAME=avogadro-60.n16.chimica.unipd.it NNODES=16, MYRANK=5, HOSTNAME=avogadro-60.n16.chimica.unipd.it NNODES=16, MYRANK=0, HOSTNAME=avogadro-22.n16.chimica.unipd.it NNODES=16, MYRANK=4, HOSTNAME=avogadro-60.n16.chimica.unipd.it NNODES=16, MYRANK=2, HOSTNAME=avogadro-22.n16.chimica.unipd.it NNODES=16, MYRANK=15, HOSTNAME=avogadro-62.n16.chimica.unipd.it NNODES=16, MYRANK=13, HOSTNAME=avogadro-62.n16.chimica.unipd.it NNODES=16, MYRANK=6, HOSTNAME=avogadro-60.n16.chimica.unipd.it NNODES=16, MYRANK=3, HOSTNAME=avogadro-22.n16.chimica.unipd.it NNODES=16, MYRANK=1, HOSTNAME=avogadro-22.n16.chimica.unipd.it NODEID=2 argc=12 NODEID=1 argc=12 NODEID=0 argc=12 NODEID=3 argc=12 :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. 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. :-) mdrun-0(mpi:[EMAIL PROTECTED]) (-: Option Filename Type Description .. When I want to delete a job, I use qdel; at this point the job desappears from queue, but apparently the job is still running on the processors. The output files are not updated and I have to enter the nodes and force killing the processes with kill -9 . This happens also if MD starts but crashes in a few seconds due for example two overlapping atoms. The job desappears from queue but is apparently running on nodes. The error message is the following: --- mpimon --- Aborting run after interrupt --- Jul 30 15:57:07:
[gmx-users] Chitosan topology
Dear gromacs users, i apply to your kind attention to know if someone have already parametrized the chitosan structure. I am trying to do it but with poor results. Can you help me? Thanking in advance Dipartimento di Medicina Sperimentale Universita' degli Studi di Parma ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Chitosan topology
Hi, Please describe clearly your poor results. Regards, Yang Ye On 7/31/2007 10:55 PM, Antonello wrote: Dear gromacs users, i apply to your kind attention to know if someone have already parametrized the chitosan structure. I am trying to do it but with poor results. Can you help me? Thanking in advance Dipartimento di Medicina Sperimentale Universita' degli Studi di Parma ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Do you need to have the parameters numbered in order?
To Whom It May Concern: Do you need to have the parameters numbered in order? For example: [ bonds ] ; aiaj functc0c1 c2c3 1 2 2 gb_16 ; CR6 (CR1) CR6 (CR1) 1.41611228368 Angstroms 1 6 2 gb_16 ; CR6 (CR1) CR6 (CR1) 1.40526545535 Angstroms 3 4 2 gb_16 ; CR6 (CR1) CR6 (CR1) 1.4138394534 Angstroms 315 2 gb_10 ; CR6 (CR1) *NRC (NR) 1.36034591189 Angstroms 4 5 2 gb_16 ; CR6 (CR1) CR6 (CR1) 1.40558244155 Angstroms 5 6 2 gb_16 ; CR6 (CR1) CR6 (CR1) 1.40420831788 Angstroms 7 8 2 gb_16 ;C2 (CR1)C2 (CR1) 1.4078362831 Angstroms 723 2 gb_3 ;C2 (CR1)H2 (HC) 1.02469166094 Angstroms 824 2 gb_3 ;C2 (CR1)H2 (HC) 1.0243183099 Angstroms 2 3 2 gb_16 ; CR6 (CR1) CR6 (CR1) 1.42527962169 Angstroms -- Notice this term is out of order. Your input would be greatly appreciated. Best wishes, Art ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] x2top GMXLIB
I have been having an odd problem that I can not seem to figure out. When running x2top in a folder within a folder in my home dir it works fine but when I go one folder deeper its gives the following error: ## Program x2top, VERSION 3.3.1 Source code file: futil.c, line: 537 Fatal error: Library file FF.dat not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) ## When it works one dir in it tells me it finds that file in the following location: Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat To make this a little clearer when I run it in: /summer07/SWNT_6_6_144/ ***it runs /summer07/SWNT_6_6_144/test***it gives that fatal error ***each of these folders are in my home dir NOTE I use the bash shell and I have the following line in my .profile file: export PATH=/usr/local/gromacs/bin:$PATH am I missing something? Or is it just something funny thing with the app? Thank you, ~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Parellel Gromacs
Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI enabled. Has anybody encountered the following error: Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file RecpAntiP-cl#1-SG-consP-L0-1-G.tpr was made for 2 nodes, while mdrun expected it to be for 1 nodes. --- Fresh Air, Green Hair (Frank Black) Halting program mdrun gcq#303: Fresh Air, Green Hair (Frank Black) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_31660: p4_error: : -1 p4_error: latest msg from perror: No such file or directory p0_31659: p4_error: : -1 I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parellel Gromacs
Have your built the GROMACS with MPI-support? Regards, Yang Ye On 8/1/2007 4:35 AM, [EMAIL PROTECTED] wrote: Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI enabled. Has anybody encountered the following error: Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file RecpAntiP-cl#1-SG-consP-L0-1-G.tpr was made for 2 nodes, while mdrun expected it to be for 1 nodes. --- Fresh Air, Green Hair (Frank Black) Halting program mdrun gcq#303: Fresh Air, Green Hair (Frank Black) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_31660: p4_error: : -1 p4_error: latest msg from perror: No such file or directory p0_31659: p4_error: : -1 I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parellel Gromacs
Hi, I am not the one who built it, but it is MPI supported. Have your built the GROMACS with MPI-support? Regards, Yang Ye On 8/1/2007 4:35 AM, [EMAIL PROTECTED] wrote: Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI enabled. Has anybody encountered the following error: Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file RecpAntiP-cl#1-SG-consP-L0-1-G.tpr was made for 2 nodes, while mdrun expected it to be for 1 nodes. --- Fresh Air, Green Hair (Frank Black) Halting program mdrun gcq#303: Fresh Air, Green Hair (Frank Black) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_31660: p4_error: : -1 p4_error: latest msg from perror: No such file or directory p0_31659: p4_error: : -1 I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parellel Gromacs
you should use the mdrun_mpi probably XAvier Hi, I am not the one who built it, but it is MPI supported. Have your built the GROMACS with MPI-support? Regards, Yang Ye On 8/1/2007 4:35 AM, [EMAIL PROTECTED] wrote: Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI enabled. Has anybody encountered the following error: Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file RecpAntiP-cl#1-SG-consP-L0-1-G.tpr was made for 2 nodes, while mdrun expected it to be for 1 nodes. --- Fresh Air, Green Hair (Frank Black) Halting program mdrun gcq#303: Fresh Air, Green Hair (Frank Black) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_31660: p4_error: : -1 p4_error: latest msg from perror: No such file or directory p0_31659: p4_error: : -1 I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Calculation of the bending modulus (Kc) of bilayer using spectral intensity.
Dear gmx-users, I'm trying to measure the bending modulus (Kc) of lipid bilayer with different sizes. I've found some papers, showing that spectral intensity needs to be calculated using the wave vector q, but couldn't understand details. I wonder if I can hear more details and how to do that using GROMACS. Any advice or suggestion will be very appreciated. Thanks, best, Hwankyu. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Do you need to have the parameters numbered in order?
Arthur Roberts wrote: To Whom It May Concern: Do you need to have the parameters numbered in order? No. Reading chapter five would tell you this. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Calculation of the bending modulus (Kc) of bilayer using spectral intensity.
Hwankyu Lee wrote: Dear gmx-users, I'm trying to measure the bending modulus (Kc) of lipid bilayer with different sizes. I've found some papers, showing that spectral intensity needs to be calculated using the wave vector q, but couldn't understand details. I wonder if I can hear more details and how to do that using GROMACS. Any advice or suggestion will be very appreciated. My guess from the limited information you've provided here is that dynamics within the molecular mechanics approximation is extremely unlikely to allow you to generate accurate observables that relate to the transmission of light. If you know about molecular dynamics already, then please elaborate in terms of the kind of observables you know you can measure... otherwise, please do some background reading about MD! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parellel Gromacs
I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename did you try the following mpirun -np 2 mdrun_mpi -deffnm filename XAvier Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
