Continuing from extended simulation fails to find output files

User discussions
1

GROMACS version: 2019.6
GROMACS modification: No

Dear all,

I have extended my simulation with the following instruction:

  1. gmx convert-tpr -s md_0_1.tpr -extend 50000 -o md_1_2.tpr
  2. gmx mdrun -deffnm md_1_2 -cpi md_0_1.cpt -noappend

It generated a bunch of .part0009 files (edr, trr etc etc)

Now, because the machine is not run 24/7, I have tried to stop and continue with the following command:

gmx mdrun -deffnm md_1_2 -s md_1_2.tpr -cpi md_1_2.cpt -append

Which throws the following error:

Output file appending has been requested,
but some output files listed in the checkpoint file md_1_2.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:
md_1_2.part0009.log
md_1_2.part0009.xtc
md_1_2.part0009.trr
md_1_2.part0009.edr

The files are indeed present in the directory, can anyone help out?

I have tried renaming the part0009 files to just md_1_2 to match -deffnm but still throws an error.

Thanks in advance for the help.

2

Could you paste all your input files?

3

Hi. I have already complete the simulation. What I did was to continue using the noappend command then merge all the xtc outputs (part0009, part0010…) together at the end of the simulation.

Thanks for trying to help though. I read somewhere by Justin saying that the append function isn’t supposed to be used for continuing an ended simulation. So I’ll just leave that as it is.

4

I’m facing the same problem can you please help how the problem was solved??

please ASAP

5

The same happened to me and I solved the problem by using the tag -deffnm
Ej:

  gmx mdrun -s inputFileName.tpr -cpi inputFileName -deffnm inputFileName

Then GROMACS is able to find the input files and append the output to them
Hope this help
Best
María

1 Like
6

Hello @yyten How did you merg the output files ?