trajin mdcrd10.gz 
#---------------------------------------------------------------#
# radius of gyration commands
#radgyr out ala10.gyr @CA time 0.0001
#---------------------------------------------------------------#
# RMS deviation commands
#rms first out ala10.rms time 0.0001 @CA
#---------------------------------------------------------------#
# sECONDARY STRUCTURE
secstruct out ala10.ss 
#---------------------------------------------------------------#
# sECONDARY STRUCTURE
#distance EE :2@CA :11@CA out ala10.EE time 0.0001
#---------------------------------------------------------------#
# hydrogen bond analysis commands
#donor mask :2-11@O
#acceptor mask :2-11@N :2-11@H
#hbond distance 3.5
#---------------------------------------------------------------#
