[gmx-users] extending simulations

[Justin Lemkul]

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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