[gmx-users] problem to continue MD run

[Mark Abraham]

Hi,

Yes, as you can see, the error message is refusing to append to files it
can't find, since appending is the default behaviour. If you continue with
mdrun -noappend then it will be fine. But you will now want to keep your
two sets of files separate and concatenate later with trjcat. Make a
backup, at least.

Mark

On Thu, 12 May 2016 22:01 Williams Miranda <williams.miranda at ucalgary.ca>
wrote:

> Hello
> This is the command line I am using:
>
> mpiexec mdrun_mpi -v -s step7_production.tpr  -cpi step7_production.cpt
> -deffnm step7_production
>
> and this is the error I get:
>
> Output file appending has been requested,
> but some output files listed in the checkpoint file step7_production.cpt
> are not present or are named differently by the current program:
> output files present: step7_production.log step7_production.xtc
> step7_production.edr
> output files not present or named differently: step7_production.trr
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 5.0.6
> Source code file:
> /RQusagers/rqchpbib/stubbsda/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c,
> line: 2640
>
> Fatal error:
> File appending requested, but 1 of the 4 output files are not present or
> are named differently
> For more information and tips for troubleshooting, please check the GROMACS
>
> Is it there any way I can continue the simulation without the *trr file?
> Thanks
> Williams
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark
> Abraham [mark.j.abraham at gmail.com]
> Sent: Thursday, May 12, 2016 1:32 AM
> To: gmx-users at gromacs.org; gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] problem to continue MD run
>
> Hi,
>
> Please report the commands you are running, and copy and paste the error
> message. Otherwise we're just wasting time guessing :-)
>
> Mark
>
> On Thu, May 12, 2016 at 4:12 AM Williams Miranda <
> williams.miranda at ucalgary.ca> wrote:
>
> > Dear GROMACS users
> > I need to continue an unfinished simulation. Because of disk space, I
> > deleted the *trr file. Unfortunately, when I try to continue the run
> using
> > the -cpi option, gromacs complains that 1 of 4 files needed to continue
> the
> > run is missing (likely, the *trr file). What could I do?
> > Regards
> > Williams
> > --
> > 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.
> >
> --
> 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.
> --
> 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.
>