[gmx-users] extending simulations

Mon Jan 29 18:02:29 CET 2018

Hi,

The following is a part of my bash script to automate extended running.
(not appending or not crashed simulations)

----------------script---------------
# em
...

# heating
...

# npt equilibration
gmx grompp -f npt.mdp -c nvt.gro -r ../mono.gro -t nvt.cpt -p ../mono.top
-n ../index.ndx -o npt.tpr
gmx mdrun -deffnm npt

# md
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p ../mono.top -n ../index.ndx
-o md1.tpr
gmx mdrun -deffnm md1

# continuous running
for i in `seq 2 6`; do
    let j=i-1
    gmx convert-tpr -s md$j.tpr -o md$i.tpr -extend 20000.0
    gmx mdrun -s md$i.tpr -cpi md$j.cpt -deffnm md$i
done
-------------script---------------

The following is the error message.

--------------------------error ----------------
Command line:
  gmx mdrun -s md2.tpr -cpi md1.cpt -deffnm md2

Output file appending has been requested,
but some output files listed in the checkpoint file md1.cpt
are not present or not named as the output files by the current program:
Expect output files present:

Expected output files not present or named differently:
  md1.log
  md1.xtc
  md1.edr

-------------------------------------------------------
Program:     gmx mdrun, version 2018
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 179)

Fatal error:
File appending requested, but 3 of the 3 output files are not present or are
named differently. For safety reasons, GROMACS-2016 and later only allows
file
appending to be used when all files have the same names as they had in the
original run. Checkpointing is merely intended for plain continuation of
runs.
For safety reasons you must specify all file names (e.g. with -deffnm), and
all these files must match the names used in the run prior to checkpointing
since we will append to them by default. If you used -deffnm and the files
listed above as not present are in fact present, try explicitly specifying
them in respective mdrun options. If the files are not available, you can
add
the -noappend flag to mdrun and write separate new parts. For mere
concatenation of files, you should use the gmx trjcat tool instead.
----------------------- error ------------------------

I did read the manual, but complicated for me.
which is input? which is output options? unclear manual for me.

I don't want appending of crashed simulation.

Previous simulation stopped regularly.

I want to run continuous md running with separate out files like md1, md2,
md3, etc

How can I achieve this goal?

Thank you.

On Mon, Jan 29, 2018 at 9:40 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> See
> http://manual.gromacs.org/documentation/2018-latest/user-guide/managing-
> simulations.html#extending-a-tpr-file
>
> Mark
>
> On Mon, Jan 29, 2018 at 3:37 PM Myunggi Yi <myunggi at pukyong.ac.kr> wrote:
>
> > Thank you for your help.
> >
> > Then how can the simulation be continued without previous cpt file
> > (information)?
> >
> > Or, should I use another way to extend the simulations?
> >
> >
> > Myunggi
> >
> >
> > On Mon, Jan 29, 2018 at 9:10 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 1/29/18 9:07 AM, Myunggi Yi wrote:
> > >
> > >> Dear users,
> > >>
> > >> I am using gromacs2018
> > >>
> > >> I've got the following error message.
> > >>
> > >>
> > >>
> > >>
> > >> Command line:
> > >>    gmx convert-tpr -s md1.tpr -f md1.cpt -n ../index.ndx -o md2.tpr
> > >> -extend
> > >> 20000.0
> > >>
> > >>
> > >> -------------------------------------------------------
> > >> Program:     gmx convert-tpr, version 2018
> > >> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
> > >> Function:    void gmx::CommandLineParser::parse(int*, char**)
> > >>
> > >> Error in user input:
> > >> Invalid command-line options
> > >>      Unknown command-line option -f
> > >>
> > >>
> > >>
> > >>
> > >> The option is valid.
> > >>
> > >> http://manual.gromacs.org/programs/gmx-convert-tpr.html
> > >>
> > >>
> > >> Is this a bug?
> > >>
> > >
> > > No, because you're looking at the wrong version of the manual.
> > >
> > > http://manual.gromacs.org/documentation/2018-latest/onlinehe
> > > lp/gmx-convert-tpr.html
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Virginia Tech Department of Biochemistry
> > >
> > > 303 Engel Hall
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalemkul at vt.edu | (540) 231-3129
> > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > >
> > > ==================================================
> > >
> > > --
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