Root mean square deviation..........

From: Gurpreet Kaur Dhindsa (
Date: Tue Aug 12 2014 - 12:58:38 CDT

 I am new in simulation and I am working on hammerhead RNA simulation.
 I am using 1RNA(1295 atoms) and 1086 water atoms. I minimized my system for 500 ps
 and equilibrated for 5 ns. I calculated RMSD which was intially increasing then it became
 flat but its value was very high around 14 Angstrom. In my configuration file, I am using
 langevin damping 1. Can someone suggest me how long should I run simulation on this system?


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