Project ID: plumID:24.011
Source: chignolin/data/template/plumed_unbiased.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes
tested onv2.10
tested onmaster
tested on master
# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

# load interface for bias computation
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=./pytorch_model_bias.cpp
#LOAD FILE=./pytorch_model_bias.so

#generated with gmx editconf -f topol.tpr -o reference.pdb, see https://www.plumed.org/doc-v2.7/user-doc/html/_m_o_l_i_n_f_o.html
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=./chignolin-ref.pdb
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-166


# Select Calpha
PROTEIN: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-166
CA: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=5,26,47,61,73,88,102,109,123,147

# RMSD
rmsd_ca: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=./chignolin-ca.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL

# END-TO-END DISTANCE
end: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,147

# HBONDS
ene: ENERGYCalculate the total potential energy of the simulation box. More details


x1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,26
x2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,47
x3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,61
x4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,73
x5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,88
x6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,102
x7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,109
x8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,123
x9: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,147
x10: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,47
x11: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,61
x12: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,73
x13: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,88
x14: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,102
x15: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,109
x16: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,123
x17: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,147
x18: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,61
x19: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,73
x20: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,88
x21: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,102
x22: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,109
x23: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,123
x24: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,147
x25: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,73
x26: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,88
x27: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,102
x28: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,109
x29: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,123
x30: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,147
x31: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,88
x32: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,102
x33: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,109
x34: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,123
x35: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,147
x36: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,102
x37: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,109
x38: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,123
x39: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,147
x40: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,109
x41: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,123
x42: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,147
x43: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,123
x44: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,147
x45: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,147

### Define positions
p1: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=5   SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
p2: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=26  SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
p3: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=47  SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
p4: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=61  SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
p5: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=73  SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
p6: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=88  SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
p7: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=102 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
p8: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=109 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
p9: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=123 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
p10: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=147 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label



#c-alpha-contacts:
cont1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=26 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=47 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=61 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=73 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=88 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=47 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont11: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=61 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont12: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=73 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont13: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=88 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont14: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont15: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont16: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont17: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont18: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=61 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont19: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=73 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont20: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=88 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont21: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont22: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont23: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont24: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont25: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=73 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont26: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=88 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont27: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont28: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont29: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont30: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont31: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=73 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=88 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont32: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=73 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont33: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=73 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont34: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=73 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont35: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=73 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont36: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=88 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont37: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=88 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont38: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=88 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont39: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=88 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont40: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=102 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont41: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=102 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont42: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=102 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont43: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=109 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont44: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=109 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
cont45: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=123 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}


cell: CELLGet the components of the simulation cell More details

#wall to prevent folding
#lwall: LOWER_WALLS ARG=rmsd_ca AT=0.3 KAPPA=500.0 EXP=2 EPS=1 OFFSET=0

# PRINT
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=*  FILEthe name of the file on which to output these quantities=COLVAR