trajin LIP4MD2_6NW.mdcrd.gz 
reference AVER_LIP4NW.pdb (where this structure was averaged over entire traj.)

box x 109.471 y 109.471 z 109.471
center :1-276 origin

rms reference mass out RMSFbytime.txt time 5 :1-265@CA
atomicfluc out RMSFbyRES.txt :1-265 byres

go