Project ID: plumID:20.034
Source: plumed_SL4.dat
Originally used with PLUMED version: 2.5.3
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

RESTART
MOLINFO STRUCTURE=SL4_ext_gmx.pdb MOLTYPE=rna

# calculate eRMSD for each helical template
ermsd0_p1: ERMSD REFERENCE=SL4_target_p1.pdb ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-41,@lcs-42,@lcs-43,@lcs-44
ermsd1_p1: ERMSD REFERENCE=SL4_target_p1.pdb ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-41,@lcs-42,@lcs-43,@lcs-44 CUTOFF=12

ermsd0_p2: ERMSD REFERENCE=SL4_target_p2.pdb ATOMS=@lcs-10,@lcs-11,@lcs-34,@lcs-35
ermsd1_p2: ERMSD REFERENCE=SL4_target_p2.pdb ATOMS=@lcs-10,@lcs-11,@lcs-34,@lcs-35 CUTOFF=12

ermsd0_p3: ERMSD REFERENCE=SL4_target_p3.pdb ATOMS=@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-30,@lcs-31,@lcs-32,@lcs-33
ermsd1_p3: ERMSD REFERENCE=SL4_target_p3.pdb ATOMS=@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-30,@lcs-31,@lcs-32,@lcs-33 CUTOFF=12

ermsd0_p4: ERMSD REFERENCE=SL4_target_p4.pdb ATOMS=@lcs-18,@lcs-19,@lcs-20,@lcs-26,@lcs-27,@lcs-28
ermsd1_p4: ERMSD REFERENCE=SL4_target_p4.pdb ATOMS=@lcs-18,@lcs-19,@lcs-20,@lcs-26,@lcs-27,@lcs-28 CUTOFF=12

# print the distance between different bases 
c1: CENTER ATOMS=@lcs-1
c2: CENTER ATOMS=@lcs-2
c3: CENTER ATOMS=@lcs-3
c4: CENTER ATOMS=@lcs-4
c5: CENTER ATOMS=@lcs-5
c6: CENTER ATOMS=@lcs-6
c7: CENTER ATOMS=@lcs-7
c8: CENTER ATOMS=@lcs-8

c10: CENTER ATOMS=@lcs-10
c11: CENTER ATOMS=@lcs-11

c13: CENTER ATOMS=@lcs-13
c14: CENTER ATOMS=@lcs-14
c15: CENTER ATOMS=@lcs-15
c16: CENTER ATOMS=@lcs-16

c18: CENTER ATOMS=@lcs-18
c19: CENTER ATOMS=@lcs-19
c20: CENTER ATOMS=@lcs-20

c26: CENTER ATOMS=@lcs-26
c27: CENTER ATOMS=@lcs-27
c28: CENTER ATOMS=@lcs-28

c30: CENTER ATOMS=@lcs-30
c31: CENTER ATOMS=@lcs-31
c32: CENTER ATOMS=@lcs-32
c33: CENTER ATOMS=@lcs-33

c34: CENTER ATOMS=@lcs-34
c35: CENTER ATOMS=@lcs-35


c37: CENTER ATOMS=@lcs-37
c38: CENTER ATOMS=@lcs-38
c39: CENTER ATOMS=@lcs-39
c40: CENTER ATOMS=@lcs-40
c41: CENTER ATOMS=@lcs-41
c42: CENTER ATOMS=@lcs-42
c43: CENTER ATOMS=@lcs-43
c44: CENTER ATOMS=@lcs-44


dp1_1: DISTANCE ATOMS=c1,c44
dp1_2: DISTANCE ATOMS=c2,c43
dp1_3: DISTANCE ATOMS=c3,c42
dp1_4: DISTANCE ATOMS=c4,c41
dp1_5: DISTANCE ATOMS=c5,c40
dp1_6: DISTANCE ATOMS=c6,c39
dp1_7: DISTANCE ATOMS=c7,c38
dp1_8: DISTANCE ATOMS=c8,c37

dp2_1: DISTANCE ATOMS=c10,c35
dp2_2: DISTANCE ATOMS=c11,c34

dp3_1: DISTANCE ATOMS=c13,c33
dp3_2: DISTANCE ATOMS=c14,c32
dp3_3: DISTANCE ATOMS=c15,c31
dp3_4: DISTANCE ATOMS=c16,c30

dp4_1: DISTANCE ATOMS=c18,c28
dp4_2: DISTANCE ATOMS=c19,c27
dp4_3: DISTANCE ATOMS=c20,c26


# here we instatiate 4 different ABMD. This is identical to one ABMD with 4 arguments,
# with the only difference that we can print the bias of each spring individually
ABMD ... 
ARG=ermsd1_p1
KAPPA=4
TO=1
LABEL=qq1 
... ABMD

ABMD ... 
ARG=ermsd1_p2
KAPPA=4
TO=1
LABEL=qq2
... ABMD

ABMD ... 
ARG=ermsd1_p3
KAPPA=4
TO=1
LABEL=qq3 
... ABMD

ABMD ... 
ARG=ermsd1_p4
KAPPA=4
TO=1
LABEL=qq4 
... ABMD

PRINT FILE=Q_YYY ARG=qq1.bias,qq2.bias,qq3.bias,qq4.bias STRIDE=5000
PRINT FILE=ERMSD_YYY ARG=ermsd0_p1,ermsd0_p2,ermsd0_p3,ermsd0_p4,ermsd1_p1,ermsd1_p2,ermsd1_p3,ermsd1_p4 STRIDE=5000
PRINT FILE=DIST_YYY ARG=dp1_1,dp1_2,dp1_3,dp1_4,dp1_5,dp1_6,dp1_7,dp1_8,dp2_1,dp2_2,dp3_1,dp3_2,dp3_3,dp3_4,dp4_1,dp4_2 STRIDE=5000