[gmx-users] Restarts with 5.0

[Mark Abraham]

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
> --
> 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-request at gromacs.org.