Project ID: plumID:20.034
Source: plumed_SL1.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

MOLINFO STRUCTURE=SL1_ext_gmx.pdb MOLTYPE=rna

# ermsd from helix 1. the large cutoff is used for pulling, the default cutoff for monitoring 
ermsd0_p1: ERMSD REFERENCE=SL1_target_p1.pdb ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29
ermsd1_p1: ERMSD REFERENCE=SL1_target_p1.pdb ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29 CUTOFF=12

# ermsd from helix 2
ermsd0_p2: ERMSD REFERENCE=SL1_target_p2.pdb ATOMS=@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21
ermsd1_p2: ERMSD REFERENCE=SL1_target_p2.pdb ATOMS=@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21 CUTOFF=12

# calculate distances between ring centers
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

c24: CENTER ATOMS=@lcs-24
c25: CENTER ATOMS=@lcs-25
c26: CENTER ATOMS=@lcs-26
c27: CENTER ATOMS=@lcs-27
c28: CENTER ATOMS=@lcs-28
c29: CENTER ATOMS=@lcs-29

c8: CENTER ATOMS=@lcs-8
c9: CENTER ATOMS=@lcs-9
c10: CENTER ATOMS=@lcs-10
c11: CENTER ATOMS=@lcs-11
c12: CENTER ATOMS=@lcs-12

c17: CENTER ATOMS=@lcs-17
c18: CENTER ATOMS=@lcs-18
c19: CENTER ATOMS=@lcs-19
c20: CENTER ATOMS=@lcs-20
c21: CENTER ATOMS=@lcs-21

dp1_1: DISTANCE ATOMS=c1,c29
dp1_2: DISTANCE ATOMS=c2,c28
dp1_3: DISTANCE ATOMS=c3,c27
dp1_4: DISTANCE ATOMS=c4,c26
dp1_5: DISTANCE ATOMS=c5,c25
dp1_6: DISTANCE ATOMS=c6,c24

dp2_1: DISTANCE ATOMS=c8,c21
dp2_2: DISTANCE ATOMS=c9,c20
dp2_3: DISTANCE ATOMS=c10,c19
dp2_4: DISTANCE ATOMS=c11,c18
dp2_5: DISTANCE ATOMS=c12,c17

# ABMD: spring constant is set to 2 kj/mol, and stops acting when reaches 1
ABMD ... 
ARG=ermsd1_p1,ermsd1_p2
KAPPA=2,2
TO=1,1 
LABEL=qq 
... ABMD

PRINT FILE=DIST_2 ARG=ermsd0_p1,ermsd0_p2,ermsd1_p1,ermsd1_p2,qq.bias,dp1_1,dp1_2,dp1_3,dp1_4,dp1_5,dp1_6,dp2_1,dp2_2,dp2_3,dp2_4,dp2_5 STRIDE=5000