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