Project ID: plumID:20.020
Source: plumed_cv.dat
Originally used with PLUMED version: 2.2
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# protein info
MOLINFO STRUCTURE=trp.pdb

# whole molecule for all the backbone atoms
WHOLEMOLECULES RESIDUES=all MOLTYPE=protein

# CA-radius of gyration
rg: GYRATION ATOMS=5,19,38,59,78,95,119,138,160,172,179,194,200,211,222,229,261,275,289,295 NOPBC

# number of backbone hydrogen bonds
COORDINATION ...
# 19 backbone oxygen atoms
GROUPA=16,35,56,75,92,116,135,157,169,176,183,197,208,219,226,250,264,278,292 
# 15 backbone hydrogen atoms
GROUPB=18,37,58,77,94,118,137,159,171,178,199,210,221,228,294
# parameters
NN=8 MM=12 R_0=0.25 NLIST NL_CUTOFF=0.8 NL_STRIDE=5 LABEL=hb NOPBC
... COORDINATION

# number of hydrophobic contacts
COORDINATION ...
# Cgamma of hydrophobic residues 
GROUPA=24,100,124,188,255,269,283
# parameters
NN=8 MM=12 R_0=0.5 LABEL=hc NOPBC
... COORDINATION

# helicity of the backbone
ALPHABETA ...
# we use as reference for phi,psi -57,-47 
ATOMS1=@phi-2 REFERENCE1=-1.0
ATOMS2=@psi-2 REFERENCE2=-0.82
ATOMS3=@phi-3 REFERENCE3=-1.0
ATOMS4=@psi-3 REFERENCE4=-0.82
ATOMS5=@phi-4 REFERENCE5=-1.0
ATOMS6=@psi-4 REFERENCE6=-0.82
ATOMS7=@phi-5 REFERENCE7=-1.0
ATOMS8=@psi-5 REFERENCE8=-0.82
ATOMS9=@phi-6 REFERENCE9=-1.0
ATOMS10=@psi-6 REFERENCE10=-0.82
ATOMS11=@phi-7 REFERENCE11=-1.0
ATOMS12=@psi-7 REFERENCE12=-0.82
ATOMS13=@phi-8 REFERENCE13=-1.0
ATOMS14=@psi-8 REFERENCE14=-0.82
ATOMS15=@phi-9 REFERENCE15=-1.0
ATOMS16=@psi-9 REFERENCE16=-0.82
ATOMS17=@phi-10 REFERENCE17=-1.0
ATOMS18=@psi-10 REFERENCE18=-0.82
ATOMS19=@phi-11 REFERENCE19=-1.0
ATOMS20=@psi-11 REFERENCE20=-0.82
ATOMS21=@phi-12 REFERENCE21=-1.0
ATOMS22=@psi-12 REFERENCE22=-0.82
ATOMS23=@phi-13 REFERENCE23=-1.0
ATOMS24=@psi-13 REFERENCE24=-0.82
ATOMS25=@phi-14 REFERENCE25=-1.0
ATOMS26=@psi-14 REFERENCE26=-0.82
ATOMS27=@phi-15 REFERENCE27=-1.0
ATOMS28=@psi-15 REFERENCE28=-0.82
ATOMS29=@phi-16 REFERENCE29=-1.0
ATOMS30=@psi-16 REFERENCE30=-0.82
ATOMS31=@phi-17 REFERENCE31=-1.0
ATOMS32=@psi-17 REFERENCE32=-0.82
ATOMS33=@phi-18 REFERENCE33=-1.0
ATOMS34=@psi-18 REFERENCE34=-0.82
ATOMS35=@phi-19 REFERENCE35=-1.0
ATOMS36=@psi-19 REFERENCE36=-0.82
LABEL=helix
... ALPHABETA

# beticity of the backbone
ALPHABETA ...
# we use as reference for phi,psi -80, +150
ATOMS1=@phi-2 REFERENCE1=-1.396
ATOMS2=@psi-2 REFERENCE2=2.618
ATOMS3=@phi-3 REFERENCE3=-1.396
ATOMS4=@psi-3 REFERENCE4=2.618
ATOMS5=@phi-4 REFERENCE5=-1.396
ATOMS6=@psi-4 REFERENCE6=2.618
ATOMS7=@phi-5 REFERENCE7=-1.396
ATOMS8=@psi-5 REFERENCE8=2.618
ATOMS9=@phi-6 REFERENCE9=-1.396
ATOMS10=@psi-6 REFERENCE10=2.618
ATOMS11=@phi-7 REFERENCE11=-1.396
ATOMS12=@psi-7 REFERENCE12=2.618
ATOMS13=@phi-8 REFERENCE13=-1.396
ATOMS14=@psi-8 REFERENCE14=2.618
ATOMS15=@phi-9 REFERENCE15=-1.396
ATOMS16=@psi-9 REFERENCE16=2.618
ATOMS17=@phi-10 REFERENCE17=-1.396
ATOMS18=@psi-10 REFERENCE18=2.618
ATOMS19=@phi-11 REFERENCE19=-1.396
ATOMS20=@psi-11 REFERENCE20=2.618
ATOMS21=@phi-12 REFERENCE21=-1.396
ATOMS22=@psi-12 REFERENCE22=2.618
ATOMS23=@phi-13 REFERENCE23=-1.396
ATOMS24=@psi-13 REFERENCE24=2.618
ATOMS25=@phi-14 REFERENCE25=-1.396
ATOMS26=@psi-14 REFERENCE26=2.618
ATOMS27=@phi-15 REFERENCE27=-1.396
ATOMS28=@psi-15 REFERENCE28=2.618
ATOMS29=@phi-16 REFERENCE29=-1.396
ATOMS30=@psi-16 REFERENCE30=2.618
ATOMS31=@phi-17 REFERENCE31=-1.396
ATOMS32=@psi-17 REFERENCE32=2.618
ATOMS33=@phi-18 REFERENCE33=-1.396
ATOMS34=@psi-18 REFERENCE34=2.618
ATOMS35=@phi-19 REFERENCE35=-1.396
ATOMS36=@psi-19 REFERENCE36=2.618
LABEL=beta
... ALPHABETA

# dihedral correlation
DIHCOR ...
ATOMS1=@phi-2,@psi-2
ATOMS2=@psi-2,@phi-3
ATOMS3=@phi-3,@psi-3
ATOMS4=@psi-3,@phi-4
ATOMS5=@phi-4,@psi-4
ATOMS6=@psi-4,@phi-5
ATOMS7=@phi-5,@psi-5
ATOMS8=@psi-5,@phi-6
ATOMS9=@phi-6,@psi-6
ATOMS10=@psi-6,@phi-7
ATOMS11=@phi-7,@psi-7
ATOMS12=@psi-7,@phi-8
ATOMS13=@phi-8,@psi-8
ATOMS14=@psi-8,@phi-9
ATOMS15=@phi-9,@psi-9
ATOMS16=@psi-9,@phi-10
ATOMS17=@phi-10,@psi-10
ATOMS18=@psi-10,@phi-11
ATOMS19=@phi-11,@psi-11
ATOMS20=@psi-11,@phi-12
ATOMS21=@phi-12,@psi-12
ATOMS22=@psi-12,@phi-13
ATOMS23=@phi-13,@psi-13
ATOMS24=@psi-13,@phi-14
ATOMS25=@phi-14,@psi-14
ATOMS26=@psi-14,@phi-15
ATOMS27=@phi-15,@psi-15
ATOMS28=@psi-15,@phi-16
ATOMS29=@phi-16,@psi-16
ATOMS30=@psi-16,@phi-17
ATOMS31=@phi-17,@psi-17
ATOMS32=@psi-17,@phi-18
ATOMS33=@phi-18,@psi-18
ATOMS34=@psi-18,@phi-19
ATOMS35=@phi-19,@psi-19
LABEL=dih
... DIHCOR

# printout
PRINT FILE=COLVAR ARG=rg,hb,hc,helix,beta,dih STRIDE=500