Project ID: plumID:20.014
Source: PLUMED_input_files/AB42_and_10074_G5/plumed/CVs.dat

#This is the metadynamics CV file for CVs on the peptide

#CV1 alpha helix
ALPHARMSD RESIDUES=1-42 TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=helix

#CV2 sum parallel and anti-parallel beta-content
PARABETARMSD RESIDUES=1-42 TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=par
ANTIBETARMSD RESIDUES=1-42 TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=anti
COMBINE ARG=par.lessthan,anti.lessthan PERIODIC=NO LABEL=beta

#CV3 radius of gyration
ca: GROUP ATOMS=5,17,27,42,62,86,103,115,126,133,154,169,185,202,219,236,258,277,293,313,333,343,358,370,386,393,404,418,440,447,457,476,495,502,521,538,554,561,568,584,600,619
rgyr: GYRATION ATOMS=ca NOPBC

#CV4 contacts between hydrophobic residues calculated as the number of Cbeta carbon couples closer than 0.6 nm 
COORDINATION GROUPA=19,44,171,260,279,295,315,335,372,449,459,478,504,523,540,570,586,602,621 R_0=0.6 NOPBC NLIST NL_CUTOFF=1.0 NL_STRIDE=20 LABEL=hydro

#CV5 the number of salt-bridges calculated as the number of couples of heavy atoms from the charged group closer than 0.6 nm 
#GROUP A is all the heavy atoms from RCOO- group of aspartic acids and glutamic acids 
#GROUP B is all the heavy atoms from RHN3+ from lysines or (RNHC(NH2)2+) of arginines
COORDINATION GROUPA=10,11,12,35,36,37,108,109,110,162,163,164,351,352,353,363,364,365 GROUPB=75,76,77,78,79,80,81,250,251,252,253,432,433,434,435 R_0=0.6 NOPBC NLIST NL_CUTOFF=1.0 NL_STRIDE=20 LABEL=salt

#CV6 correlation between consecutive psi torsion angles.
DIHCOR ...
ATOMS1=@psi-1,@psi-2
ATOMS2=@psi-2,@psi-3
ATOMS3=@psi-3,@psi-4
ATOMS4=@psi-4,@psi-5
ATOMS5=@psi-5,@psi-6
ATOMS6=@psi-6,@psi-7
ATOMS7=@psi-7,@psi-8
ATOMS8=@psi-8,@psi-9
ATOMS9=@psi-9,@psi-10
ATOMS10=@psi-10,@psi-11
ATOMS11=@psi-11,@psi-12
ATOMS12=@psi-12,@psi-13
ATOMS13=@psi-13,@psi-14
ATOMS14=@psi-14,@psi-15
ATOMS15=@psi-15,@psi-16
ATOMS16=@psi-16,@psi-17
ATOMS17=@psi-17,@psi-18
ATOMS18=@psi-18,@psi-19
ATOMS19=@psi-19,@psi-20
ATOMS20=@psi-20,@psi-21
ATOMS21=@psi-21,@psi-22
ATOMS22=@psi-22,@psi-23
ATOMS23=@psi-23,@psi-24
ATOMS24=@psi-24,@psi-25
ATOMS25=@psi-25,@psi-26
ATOMS26=@psi-26,@psi-27
ATOMS27=@psi-27,@psi-28
ATOMS28=@psi-28,@psi-29
ATOMS29=@psi-29,@psi-30
ATOMS30=@psi-30,@psi-31
ATOMS31=@psi-31,@psi-32
ATOMS32=@psi-32,@psi-33
ATOMS33=@psi-33,@psi-34
ATOMS34=@psi-34,@psi-35
ATOMS35=@psi-35,@psi-36
ATOMS36=@psi-36,@psi-37
ATOMS37=@psi-37,@psi-38
ATOMS38=@psi-38,@psi-39
ATOMS39=@psi-39,@psi-40
ATOMS40=@psi-40,@psi-41
LABEL=dihcor
NOPBC
... DIHCOR