The single code from script reproduced the same error: C
*ommand line: gmx grompp -f /home/Documents/tutorial/MDP/EM/em_steep.mdp -c /home/Documents/tutorial/Methane/methane_water.gro -p /home/Documents/tutorial/Methane/topol.top -o min.tpr-------------------------------------------------------Program gmx, VERSION 5.0Source code file: /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/futil.cpp, line: 540File input/output error:/home/Documents/tutorial/MDP/EM/em_steep.mdpFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors <http://www.gromacs.org/Documentation/Errors>-------------------------------------------------------GROMACS: gmx mdrun, VERSION 5.0GROMACS 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 Peter Kasson 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 Christian Wennberg Maarten Wolf and the project leaders:Mark Abraham, Berk Hess, Erik Lindahl, and David van der SpoelCopyright (c) 1991-2000, University of Groningen, The Netherlands.Copyright (c) 2001-2014, The GROMACS development team atUppsala University, Stockholm University andthe Royal Institute of Technology, Sweden.check out http://www.gromacs.org <http://www.gromacs.org> for more information.GROMACS is free software; you can redistribute it and/or modify itunder the terms of the GNU Lesser General Public Licenseas published by the Free Software Foundation; either version 2.1of the License, or (at your option) any later version.GROMACS: gmx mdrun, VERSION 5.0Executable: /usr/local/gromacs/bin/gmxLibrary dir: /usr/local/gromacs/share/gromacs/topCommand line: mdrun -nt 2 -deffnm min0Back Off! I just backed up min0.log to ./#min0.log.5#-------------------------------------------------------Program mdrun, VERSION 5.0Source code file: /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513Can not open file:min0.tprFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentati <http://www.gromacs.org/Documentati>* on/Errors ------------------------------------------------------- However, I tried using normal command i.e. I dint use the script and the command worked smoothly. The minimization step is complete. I dont know why there is "File input/output" error. I have placed the .mdp files in /home/Docuemnts/tutorial/MDP/EM, as I mentioned in .sh file: #!/bin/bash # Set some environment variables FREE_ENERGY=/home/Documents/tutorial echo "Free energy home directory set to $FREE_ENERGY" MDP=$FREE_ENERGY/MDP/EM echo ".mdp files are stored in $MDP" LAMBDA=0 # A new directory will be created for each value of lambda and # at each step in the workflow for maximum organization. mkdir Lambda_$LAMBDA cd Lambda_$LAMBDA ################################# # ENERGY MINIMIZATION 1: STEEP # ################################# echo "Starting minimization for lambda = $LAMBDA..." mkdir EM_1 cd EM_1 # Iterative calls to grompp and mdrun to run the simulations gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/Methane/methane_water.gro -p $FREE_ENERGY/Methane/topol.top -o min$LAMBDA.tpr mdrun -nt 2 -deffnm min$LAMBDA sleep 10 Have I messed up the job.sh? On Fri, Sep 2, 2016 at 7:28 PM, Nikhil Maroli <scinik...@gmail.com> wrote: > run the single code from script and see what prints on the screen,that's > what Justin suggested > -- > 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. > -- 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.
