[gmx-users] Restarts with 5.0

[Ali Khan]

Fair enough. Thank you.


On Thu, Jul 3, 2014 at 3:26 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Jul 3, 2014 7:07 PM, "Ali Khan" <akk5r at virginia.edu> wrote:
> >
> > 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?
>
> Yes, but as the message says, you're not allowed to append to the files.
> And your paper's reviewer would laugh at you for switching method
> mid-experiment unless you do a lot work to show the difference was
> immaterial. So, generally, you should not consider such a switch.
>
> Mark
>
> > 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
> > 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 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
> > OMP_NUM_THREADS to 12*
> >
> > *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:
> > 2029*
> >
> > *Fatal error:*
> > *Output file appending requested, but input and checkpoint states are not
> > identical.*
> > *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
> > GROMACS*
> > *website at http://www.gromacs.org/Documentation/Errors
> > <http://www.gromacs.org/Documentation/Errors>*
> > *-------------------------------------------------------*
> >
> > Best Wishes,
> > Ali Khan
> > --
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