Project ID: plumID:20.034
Source: plumed_SL23.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=SL_23_ext_gmx.pdb MOLTYPE=rna

ermsd_full: ERMSD REFERENCE=SL_23_stem2_gmx.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_sl2: ERMSD REFERENCE=SL_23_stem2_gmx.pdb ATOMS=@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16 

ermsd_sl2_target: ERMSD REFERENCE=SL_23_stem2_gmx.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_sl3: ERMSD REFERENCE=SL_23_stem3_gmx.pdb ATOMS=@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-29,@lcs-30,@lcs-31,@lcs-32

ermsd_sl3_target: ERMSD REFERENCE=SL_23_stem3_gmx.pdb ATOMS=@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-29,@lcs-30,@lcs-31,@lcs-32 CUTOFF=12



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

c18: CENTER ATOMS=@lcs-2
c19: CENTER ATOMS=@lcs-3
c20: CENTER ATOMS=@lcs-4
c21: CENTER ATOMS=@lcs-5

c29: CENTER ATOMS=@lcs-12
c30: CENTER ATOMS=@lcs-13
c31: CENTER ATOMS=@lcs-14
c32: CENTER ATOMS=@lcs-15


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
d7: DISTANCE ATOMS=c18,c32
d8: DISTANCE ATOMS=c19,c31
d9: DISTANCE ATOMS=c20,c30
d10: DISTANCE ATOMS=c21,c29

ABMD ... 
ARG=ermsd_sl2_target,ermsd_sl3_target
KAPPA=2,2
TO=1,1 
LABEL=qq 
... ABMD

PRINT FILE=DIST_K_YY_XX ARG=ermsd_full,ermsd_sl2,ermsd_sl2_target,ermsd_sl3,ermsd_sl3_target STRIDE=5000
PRINT FILE=OT_K_YY_XX  ARG=qq.bias,d1,d2,d3,d4,d5,d6,d7,d8,d9,d10 STRIDE=5000