From: zoran matovic (
Date: Sat Feb 25 2017 - 13:40:12 CST

Dear VMD users,

I ran 60 ns NAMD trajectory of protein dimmer. RMSD calculated by VMD is attached. RMSD spikes are obviously due to the periodic box and the system appeared to be equilibrated. I turned on “wrapAll” option in config file. Protein monomers stacked together but due to PB transition I have rmsd spikes. May be some of u people know how to eliminate these spikes?