PLUMED-NEST

Project ID: plumID:20.034
Source: plumed_SL5A.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=SL5a_ext_gmx.pdb MOLTYPE=rna


ermsd0_p1: ERMSD REFERENCE=SL5a_H1_template.pdb ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33
ermsd1_p1: ERMSD REFERENCE=SL5a_H1_template.pdb ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33 CUTOFF=12

ermsd0_p2: ERMSD REFERENCE=SL5a_H2_template.pdb ATOMS=@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24
ermsd1_p2: ERMSD REFERENCE=SL5a_H2_template.pdb ATOMS=@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24 CUTOFF=12


# HELIX1 
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

c27: CENTER ATOMS=@lcs-27
c28: CENTER ATOMS=@lcs-28
c29: CENTER ATOMS=@lcs-29
c30: CENTER ATOMS=@lcs-30
c31: CENTER ATOMS=@lcs-31
c32: CENTER ATOMS=@lcs-32
c33: CENTER ATOMS=@lcs-33

# HELIX2
c9: CENTER ATOMS=@lcs-9
c10: CENTER ATOMS=@lcs-10
c11: CENTER ATOMS=@lcs-11
c12: CENTER ATOMS=@lcs-12
c13: CENTER ATOMS=@lcs-13

c20: CENTER ATOMS=@lcs-20
c21: CENTER ATOMS=@lcs-21
c22: CENTER ATOMS=@lcs-22
c23: CENTER ATOMS=@lcs-23
c24: CENTER ATOMS=@lcs-24


dp1_1: DISTANCE ATOMS=c1,c33
dp1_2: DISTANCE ATOMS=c2,c32
dp1_3: DISTANCE ATOMS=c3,c31
dp1_4: DISTANCE ATOMS=c4,c30
dp1_5: DISTANCE ATOMS=c5,c29
dp1_6: DISTANCE ATOMS=c6,c28
dp1_7: DISTANCE ATOMS=c7,c27

dp2_1: DISTANCE ATOMS=c9,c24
dp2_2: DISTANCE ATOMS=c10,c23
dp2_3: DISTANCE ATOMS=c11,c22
dp2_4: DISTANCE ATOMS=c12,c21
dp2_5: DISTANCE ATOMS=c13,c20


# other 
c8: CENTER ATOMS=@lcs-8
c14: CENTER ATOMS=@lcs-14
c15: CENTER ATOMS=@lcs-15
c18: CENTER ATOMS=@lcs-18
c19: CENTER ATOMS=@lcs-19
c25: CENTER ATOMS=@lcs-25
c26: CENTER ATOMS=@lcs-26

D8_25: DISTANCE ATOMS=c8,c25
D8_26: DISTANCE ATOMS=c8,c26
D14_19: DISTANCE ATOMS=c14,c19
D15_18: DISTANCE ATOMS=c15,c18

chi: TORSION ATOMS=@chi-18

ABMD ... 
ARG=ermsd1_p1,ermsd1_p2
KAPPA=1,1
TO=1,1 
LABEL=qq 
... ABMD

PRINT FILE=ERMSD_YYY ARG=ermsd0_p1,ermsd0_p2,ermsd1_p1,ermsd1_p2,qq.bias STRIDE=5000
PRINT FILE=DIST_YYY ARG=dp1_1,dp1_2,dp1_3,dp1_4,dp1_5,dp1_6,dp1_7,dp2_1,dp2_2,dp2_3,dp2_4,dp2_5,D8_25,D8_26,D14_19,D15_18,chi STRIDE=5000