[gmx-users] Restarts with 5.0

Ali Khan akk5r at virginia.edu
Thu Jul 3 19:07:24 CEST 2014

Hi Everyone,

I have a simulation running with gromacs 4.6.5. Is it possible to stop the
simulation and restart from a check point with version 5.0? I attempted to
do it and got the following output:

*GROMACS:    gmx mdrun, VERSION 5.0*

*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 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 Spoel*

*Copyright (c) 1991-2000, University of Groningen, The Netherlands.*
*Copyright (c) 2001-2014, The GROMACS development team at*
*Uppsala University, Stockholm University and*
*the Royal Institute of Technology, Sweden.*
*check out http://www.gromacs.org <http://www.gromacs.org> for more

*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 mdrun, VERSION 5.0*
*Executable:   /home/akk5r/gromacs/bin/gmx*
*Library dir:  /home/akk5r/gromacs/share/gromacs/top*
*Command line:*
*  mdrun -v -maxh 168 -nt 12 -deffnm md_0_100 -cpi md_0_100.cpt*

*Reading file md_0_100.tpr, VERSION 4.6.5 (single precision)*
*Note: file tpx version 83, software tpx version 100*
*Changing nstlist from 5 to 25, rlist from 1.2 to 1.223*

*The number of OpenMP threads was set by environment variable

*Reading checkpoint file md_0_100.cpt generated: Thu Jul  3 00:38:43 2014*

*Program mdrun, VERSION 5.0*
*Source code file:
/home/akk5r/Downloads/gromacs-5.0/src/gromacs/gmxlib/checkpoint.c, line:

*Fatal error:*
*Output file appending requested, but input and checkpoint states are not
*Stopping the run to prevent you from ruining all your data...*
*You can try with the -noappend option, and get more info in the log file.*

*For more information and tips for troubleshooting, please check the
*website at http://www.gromacs.org/Documentation/Errors

Best Wishes,
Ali Khan

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