Creating optional .xtc trajectory file with mdrun

User discussions
1

GROMACS version: 2022.3
GROMACS modification: Yes (compiled with plumed-2.8.1 in a cluster system)

Hi,
I am doing MD simulation and I want to create .xtc trajectory in addition to the default -mdrun option (.trr) so I wont need to use trjconv later for video representation.
I am using this command:
mpirun -np 1 gmx_mpi mdrun -v -deffnm {curr_step} -x {curr_step}.xtc -plumed plumed_n.dat -nb gpu -pme gpu -bonded gpu
The relevant part is “-x ${curr_step}.xtc” that is being ignored, although the other files are generated normally (log, edr, trr, cpt, gro and tpr files).
The -mdrun command documentation doesn’t specify a hint as to why it happens (or I missed it).
What do I do wrong? Or you cant generate them both in one run?

Thank you,
David.

2

An .xtc file is only written when a non-zero value is given to nstxout-compressed in the .mdp file. It is not determined by supplying the -x option to mdrun.

3

Now I understand why it was generated in equilibration - it was switched automatically from older version argument:
"Replacing old mdp entry ‘nstxtcout’ by ‘nstxout-compressed’ "

Thank you!