How to quickly extract all structures with the specified time frames in the 300-ns MD simulation?

GROMACS version:2021.1
GROMACS modification: No

Hello,

After runing gmx cluster, I want to extract all structures (either in the seperate pdbs or in one pdb with all structures) in the maximum cluster.

I did it like this (the maximum cluster includes 66 time frames (or structures) and I want to extract them all as pdb format):

for i in {222,232.5,233,233.5,234,234.5,235,235.5,236.5,237,237.5,
238,239,239.5,240,241.5,242,242.5,243,243.5,244,244.5,245,245.5,246,
246.5,247,247.5,248,248.5,249,249.5,250,250.5,251,251.5,252,252.5,253,
253.5,254,254.5,255,255.5,256,256.5,257,257.5,258.5,259,259.5,260,260.5,
261.5,262.5,264.5,265.5,266,267.5,268.5,269,
270,270.5,271,272,273}; do echo 1 | gmx trjconv -s md_300ns.tpr -f md_300ns_noPBC.xtc -tu ns -dump $i -o clust_mulstr_$i.pdb; done

But I found that it is too slow to extract them all. Each time it read information from beginning.

Are there smart ways to do the same task quickly?

Thanks,
Ming

HI,
you can try to use the gmx cluster option -cl -wcl 1 -nst 1
Best regards
Alessandra

@alevilla

Thanks for your help.

I will check that.

Ming