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

User discussions
1

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

2

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

3

@alevilla

Thanks for your help.

I will check that.

Ming