[gmx-users] Problems with continuing simulation after time limit

[Searle Duay]

Hi everyone,

I am running a simulation of 500 ns using GROMACS 2016 through submitting
jobs in our HPC. Due to limited time to run per job, I wrote a bash code to
resubmit the job and resume the simulation from  a checkpoint. However, I
am receiving an error when the following command is run:

Command line:
 gmx_mpi mdrun -s /scratch/sad16109/clavanin/copy/gromacs/part1/part1.tpr
-deffnm /scratch/sad16109/clavanin/copy/gromacs/part2/neutral2 -cpi
/scratch/sad16109/clavanin/copy/gromacs/part1/part1.cpt -cpt 100 -cpo
/scratch/sad16109/clavanin/copy/gromacs/part2/part2.cpt -maxh 12

the error being issued is:

Output file appending has been requested,
but some output files listed in the checkpoint file
/scratch/sad16109/clavanin/copy/gromacs/part1/part1.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:
 /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.log
 /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.trr
 /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.edr

-------------------------------------------------------
Program:     gmx mdrun, version 2016
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)
MPI rank:    0 (out of 24)

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 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.

I receive that error even if the neutral1.log, neutral1.trr, and
neutral1.edr files are present in the "part1" folder. I was using the
similar code with Gromacs 5 and I am not having problems. I am not sure if
this is something new in Gromacs 2016.

I am thinking that there might be something wrong with how I name my files
but I am not sure where.

Thanks!

-- 
Searle Aichelle S. Duay
Ph.D. Student
Chemistry Department, University of Connecticut
searle.duay at uconn.edu