trajin ../d4g_ALL_FRAMES.mdcrd
# Get H-H distance info 
distance H-H1 :4@H :12@H2N out Distance_H-H_Explicit_1_cpptraj.out 
distance H-H2 :5@H :13@H2N out Distance_H-H_Explicit_2_cpptraj.out 
distance H-H3 :6@H :14@H2N out Distance_H-H_Explicit_3_cpptraj.out 
distance H-H4 :7@H :15@H2N out Distance_H-H_Explicit_4_cpptraj.out 
# Get O-O distance info 
distance O-O1 :4@OG1 :4@O out Distance_O-O_Explicit_1_cpptraj.out 
distance O-O2 :5@OG1 :5@O out Distance_O-O_Explicit_2_cpptraj.out 
distance O-O3 :6@OG1 :6@O out Distance_O-O_Explicit_3_cpptraj.out 
distance O-O4 :7@OG1 :7@O out Distance_O-O_Explicit_4_cpptraj.out 
go
