[gmx-users] Restart

Eric Smoll ericsmoll at gmail.com
Tue Jul 31 04:14:00 CEST 2018

Hello GROMACS users,

I had a simulation terminate unexpectedly very close to completion and I
would like to resume the simulation from a checkpoint file.

my mdrun flags are -cpi, -s, -o, -x, -c, -e, -g, and -cpo.
All of the associated files are present (except the -c file since there was
a crash).  Looking at the last saved checkpoint in the log file and running
"gmx check -f state.cpt" on the cpo file "state.cpt" confirms that the
proper time has been saved.  An important point is that the files names I
provided are not used because gromacs has added the infix ".part0001"

The GROMACS 2016 page on "Managing Long Simulations" claims I can restart
with the command "gmx mdrun -cpi state.cpt."  However, this starts the
simulation at step 0 and does not append to the current file (instead
adding to a file without the ".part0001" infix).  It is unclear if this
will only execute the remaining number of steps or not.

How can I get mdrun to launch this restart correctly?


More information about the gromacs.org_gmx-users mailing list