[gmx-users] extending simulations

[Mark Abraham]

Hi,

Further to what Justin said, I see a lot of people crafting complex bash
scripts to run their whole project in the same directory, and as part of
that the scripts do approximately what

gmx mdrun -cpi -noappend

does - name the output files so that they include a part number, and will
need to be manually appended later. Where's the value for the extra work?
If you put your equilibration and simulation in different directories, you
can use the default file naming and not create problems. :-)

Mark

On Tue, Jan 30, 2018 at 2:16 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/29/18 12:01 PM, Myunggi Yi wrote:
> > 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
>
> md1.cpt specifies that all your output files should have "md1" as their
> prefix. You're simultaneously trying to change names (via -deffnm md2)
> and append (because -append is default) to files named md.*  Those
> options are mutually exclusive. If you change file names, use -noappend
> and get a new set of output files that can be appended later.
>
> -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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