# This reads in the template pdb file and thus allows us to use the @nonhydrogens
# special group later in the input
MOLINFO STRUCTURE=beta-hairpin.pdb MOLTYPE=protein

# This stores the positions of all the nonhydrogen atoms for later analysis
cc: COLLECT_FRAMES ATOMS=@nonhydrogens
# This should output the atomic positions for the frames that were collected and analyzed using MDS
OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=cc FILE=traj.pdb

# The following commands compute all the Ramachandran angles of the protein for you
r2-phi: TORSION ATOMS=@phi-2
r2-psi: TORSION ATOMS=@psi-2
r3-phi: TORSION ATOMS=@phi-3
r3-psi: TORSION ATOMS=@psi-3
r4-phi: TORSION ATOMS=@phi-4
r4-psi: TORSION ATOMS=@psi-4
r5-phi: TORSION ATOMS=@phi-5 
r5-psi: TORSION ATOMS=@psi-5 
r6-phi: TORSION ATOMS=@phi-6 
r6-psi: TORSION ATOMS=@psi-6 
r7-phi: TORSION ATOMS=@phi-7 
r7-psi: TORSION ATOMS=@psi-7 
r8-phi: TORSION ATOMS=@phi-8 
r8-psi: TORSION ATOMS=@psi-8 
r9-phi: TORSION ATOMS=@phi-9 
r9-psi: TORSION ATOMS=@psi-9 
r10-phi: TORSION ATOMS=@phi-10  
r10-psi: TORSION ATOMS=@psi-10  
r11-phi: TORSION ATOMS=@phi-11  
r11-psi: TORSION ATOMS=@psi-11  
r12-phi: TORSION ATOMS=@phi-12  
r12-psi: TORSION ATOMS=@psi-12  
r13-phi: TORSION ATOMS=@phi-13  
r13-psi: TORSION ATOMS=@psi-13  
r14-phi: TORSION ATOMS=@phi-14  
r14-psi: TORSION ATOMS=@psi-14  
r15-phi: TORSION ATOMS=@phi-15  
r15-psi: TORSION ATOMS=@psi-15  
r16-phi: TORSION ATOMS=@phi-16  
r16-psi: TORSION ATOMS=@psi-16  

# This command stores all the Ramachandran angles that were computed
angles: COLLECT_FRAMES ARG=r2-phi,r2-psi,r3-phi,r3-psi,r4-phi,r4-psi,r5-phi,r5-psi,r6-phi,r6-psi,r7-phi,r7-psi,r8-phi,r8-psi,r9-phi,r9-psi,r10-phi,r10-psi,r11-phi,r11-psi,r12-phi,r12-psi,r13-phi,r13-psi,r14-phi,r14-psi,r15-phi,r15-psi,r16-phi,r16-psi
# Lets now compute the matrix of distances between the frames in the space of the Ramachandran angles
distmat: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=angles METRIC=EUCLIDEAN
# Now select 500 landmark points to analyze
fps: LANDMARK_SELECT_FPS USE_OUTPUT_DATA_FROM=distmat NLANDMARKS=500
# Run MDS on the landmarks
mds: CLASSICAL_MDS USE_OUTPUT_DATA_FROM=fps NLOW_DIM=2
# Project the remaining trajectory data
osample: PROJECT_ALL_ANALYSIS_DATA USE_OUTPUT_DATA_FROM=distmat PROJECTION=mds

# This command outputs all the projections of all the points in the low dimensional space
OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=osample ARG=osample.* FILE=mds_data

# These next three commands calculate the secondary structure variables.  These
# variables measure how much of the structure resembles an alpha helix, an antiparallel beta sheet
# and a parallel beta sheet.  Configurations that have different secondary structures should be projected
# in different parts of the low dimensional space.
alpha: ALPHARMSD RESIDUES=all
abeta: ANTIBETARMSD RESIDUES=all STRANDS_CUTOFF=1.0
pbeta: PARABETARMSD RESIDUES=all STRANDS_CUTOFF=1.0

# These commands collect and output the secondary structure variables so that we can use this information to
# determine how good our projection of the trajectory data is.
cc2: COLLECT_FRAMES ARG=alpha,abeta,pbeta
OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=cc2 ARG=cc2.* FILE=secondary_structure_data