[gmx-users] gmx cluster cut off

RJ rajiv at kaist.ac.kr
Wed Aug 12 09:51:57 CEST 2015

Dear all,

I have done protein with three different inhibitor for 100ns simulation and would use the most populated structure for further analysis.

What i wonder is how do i select the perfect cut off value to choose the most populated structure from 100ns? Is that following command can provide the a single structure to do my further analysis?

"gmx cluster -f prd_noPBC.xtc -s prd.tpr -o cluster.xpm -minstruct 10 -sz cluster-sizes.xvg -clid cluster-over-time.xvg -cl clusters.pdb -method gromos -dist rms-dist.xvg -noav -cutoff 0.25

I just confused which cut off value i should give to obtain the center most populated structure ?

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