[gmx-users] sampling conformation on the basis of RMSD value

vivek sharma viveksharma.iitb at gmail.com
Wed Sep 17 15:36:17 CEST 2008

Hi There,
I have a 5 nsec trajectory file for my system...and a RMSD plot for the
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,
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