Hi There, I have a 5 nsec trajectory file for my system...and a RMSD plot for the same. while doing simulation I have sampled the frame at each 500 ps, Now I want to choose conformation on the basis of RMSD values, like conformation which has RMSD difference of some value say A nanometer. Can anybody suggest me a way to do the same ?
I heard of g-cluster command for the same, but don't know how can I use it for given RMSD difference ? Can I do it before giving the final run command, so it will sample the conformation during the run on the basis of RMSD value ? With Thanks, Vivek
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