[gmx-users] RMSD per residue

Saman Shahriyari samanshahriyari at yahoo.com
Thu Dec 19 12:03:17 CET 2013

Dear users
I am trying to have the "RMSD per residue" profile of my trajectory. i approached this by using "g_rmsf" tool with "-od" and "-res" options. although i can have such profile, but it seems that the average structure of my trajectory is being chosen as the reference to measure deviations from. if it is the case, is there any way i can use the starting structure of trajectory as the reference structure to have a profile of RMSD pre residue by g_rmsf tool (or any other tool)? in fact I am trying to know how much of deviation each residue has experienced through the simulation time.  

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