Restart without .xtc file

User discussions
1

GROMACS version: 2021.3
GROMACS modification: No

Hi,

I was wonder if it possible to restart and/or extend a simulation without a .xtc trajectory file.

Following the documentation, I should be able to do something like this:
gmx grompp -f grompp-noxtc.mdp -c original.gro -p topology.top -t state.cpt -o system-noxtc.tpr
Where in grompp-noxtc.mdp I set nstxtcout = 0.

However… It doesn’t work. Upon running:
mdrun -s system-noxtc.tpr -cpi state.cpt -nsteps 250000000
I get the following error message:

Inconsistency in user input:
Some output files listed in the checkpoint file state.cpt are not present or
not named as the output files by the current program:)
Expected output files that are present:
  md.log
  traj.trr
  ener.edr

Expected output files that are not present or named differently:
  traj.xtc

What am I doing wrong?

Michele

P.S. -noappend is not an option: I need to append to energy.edr

3

Update: I tried to ‘trick’ Gromacs by placing a dummy traj.xtc file. The error is still present:

Expected output files that are not present or named differently:
  traj.xtc
4

Final update: I ““solved”” the problem by manually commenting some lines of code in handlerestart.cpp.

This is of course not a safe, let alone elegant, solution to the problem. I can imagine the case where a user has collected enough trajectory frames and only want to extend the collection of energy observables, or vice versa. Shouldn’t Gromacs leave the choice of what to append to and what not to the user?

Michele

5

A simple solution is to use the -noappend flag and use gmx eneconv to concatenate the energy files without losing information.