[gmx-users] Issue with RMSD profile

Sainitin Donakonda saigro16 at gmail.com
Fri Apr 26 15:33:22 CEST 2013

Hello all,

I ran 10ns molecular dynamics simulation of protein ligand complex ..in
which protein homology model..finally i analyzed .xtc file which is
produced after MD production run..first i plotted RMSD profile of backbone
of the protein ..it show that line starts from 0.2 nm to 0.4 nm and from it
is stabilized in plateau..

My question is  fluctuation in RMSD profile from 0.2nm to 0.4 nm is
acceptable range or not?

Can any body explain this

Thank you very much


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