Writing output to a particular directory

User discussions
1

GROMACS version: 2022.5
GROMACS modification: No

Hello everyone,

Does GROMACS allow for output to be written to a defined directory path? As can be seen in the code snippet below, I want the gmx cluster output to be written to different directories named on the RMSD cutoff used for clustering.

Please let me know if this approach sounds reasonable. Otherwise, how should I proceed with this? Thanks a lot for your assistance.

for i in $(seq 0.05 0.05 1.00)

do 
  
  mkdir -p $i

  gmx cluster -f md.trr -s md.tpr -method gromos -cutoff $i -n cluster.ndx -cl $i/cluster.gro

done
2

This worked without any hassles, gmx can write the output to the folder location provided in the shell script.