Project ID: plumID:20.034
Source: plumed_SL2.dat
Originally used with PLUMED version: 2.5.3
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

RESTART
MOLINFO STRUCTURE=SL2_ref.pdb MOLTYPE=rna

# in this case we can monitor the distance from the reference NMR structure
ermsd0: ERMSD REFERENCE=SL2_NMR_template.pdb ATOMS=@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16 

ermsd_target: ERMSD REFERENCE=SL2_match.pdb ATOMS=@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16 CUTOFF=12
ermsd_target0: ERMSD REFERENCE=SL2_match.pdb ATOMS=@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16

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

c10: CENTER ATOMS=@lcs-10
c12: CENTER ATOMS=@lcs-12
c13: CENTER ATOMS=@lcs-13
c14: CENTER ATOMS=@lcs-14
c15: CENTER ATOMS=@lcs-15
c16: CENTER ATOMS=@lcs-16

d1: DISTANCE ATOMS=c2,c16
d2: DISTANCE ATOMS=c3,c15
d3: DISTANCE ATOMS=c4,c14
d4: DISTANCE ATOMS=c5,c13
d5: DISTANCE ATOMS=c6,c12
d6: DISTANCE ATOMS=c7,c10

ABMD ... 
ARG=ermsd_target 
KAPPA=2.0
TO=1
LABEL=qq0 
... ABMD


PRINT FILE=DIST_YYY ARG=ermsd0,ermsd_target,ermsd_target0,d1,d2,d3,d4,d5,d6,qq0.bias STRIDE=5000