[gmx-users] problem to continue MD run

[Williams Miranda]

Many thanks!
________________________________________
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 2:06 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] problem to continue MD run

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
> > --
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