PLUMED-NEST by plumed-nest

Project ID: plumID:26.017
Source: C-tail_detachment/0/plumed.dat
Originally used with PLUMED version: 2.9.1
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
#RESTART
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../LinearGhost.so
The LOAD action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../HBondsOMP.so
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../CoordinationMapOMP.so

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=../folded_protein.pdb
WO: 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=6621-154857:3
The GROUP action with label WO calculates somethingWH: 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=6622-154858:3,6623-154859:3
The GROUP action with label WH calculates somethingrmsd_ca: RMSDCalculate the RMSD with respect to a reference structure. More details TYPE the manner in which RMSD alignment is performed=OPTIMAL REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../folded_protein_CA.pdb

The RMSD action with label rmsd_ca calculates the following quantities: Quantity    Description  
rmsd_ca.value the RMSD distance between the instantaneous structure and the reference structure/s that were inputcmapH_sum: HBONDSThis action is not part of PLUMED and was included by using a LOAD command More details ...
   ATOMS1=107,6170,106,6169 SWITCH1={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8} ANGLE1=1 WEIGHT1=1.0
   ATOMS2=143,6205,142,6204 SWITCH2={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8} ANGLE2=1 WEIGHT2=1.0
   ATOMS3=6192,121,6191,120 SWITCH3={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8} ANGLE3=1 WEIGHT3=1.0
   ATOMS4=6156,81,6155,80 SWITCH4={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8} ANGLE4=1 WEIGHT4=1.0
   ATOMS5=6219,163,6218,162 SWITCH5={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8} ANGLE5=1 WEIGHT5=1.0
   ATOMS6=69,6135,68,6134 SWITCH6={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8} ANGLE6=1 WEIGHT6=1.0
   ATOMS7=159,6215,158,6214 SWITCH7={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8} ANGLE7=0 WEIGHT7=1.0
   SUM
...

VA_H_107-O_6170: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=6169,6170,6171 COORDINATES=0.25
VH_H_107-O_6170: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=106,107,108 COORDINATES=0.25
VA_H_143-O_6205: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=6204,6205,6206 COORDINATES=0.25
VH_H_143-O_6205: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=142,143,144 COORDINATES=0.25
VA_H_6192-O_121: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=120,121,122 COORDINATES=0.25
VH_H_6192-O_121: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=6191,6192,6193 COORDINATES=0.25
VA_H_6156-O_81: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=80,81,82 COORDINATES=0.25
VH_H_6156-O_81: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=6155,6156,6157 COORDINATES=0.25
VA_H_6219-O_163: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=162,163,164 COORDINATES=0.25
VH_H_6219-O_163: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=6218,6219,6220 COORDINATES=0.25
VA_H_69-O_6135: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=6134,6135,6136 COORDINATES=0.25
VH_H_69-O_6135: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=68,69,70 COORDINATES=0.25
VA_HZ1_159-OD2_6215: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=6214,6215,6216 COORDINATES=0.25
VH_HZ1_159-OD2_6215: LINEARGHOSTThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=158,159,160 COORDINATES=0.25

hbnnc_test: COORDINATIONMAPThis action is not part of PLUMED and was included by using a LOAD command More details ...
   GROUPA1=VH_HZ1_159-OD2_6215 GROUPB1=6214,6206,6205,163,6190,6191,6218,142,164,6217,186,121,185,6171,6238,141,6202,6203,195,122,6170,6247,6237,106,180,6155,6154,105,95,81,101,82,98,6136,6135,68,6123,74,6124,6112,6121,6120,6133,6132 SWITCH1={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5}
   GROUPA2=VH_H_6156-O_81 GROUPB2=105,6135,74,6136,6154,6171,95,121,98,6191,122,6124,101,6190,6123,6202,6203,6205,6112,6133,6132,141,142,6206,6217,6121,158,6218,6120,163,6215,164,6214,6237,6238,6247,185,186,195,180
   GROUPA3=VH_H_69-O_6135 GROUPB3=74,81,6124,6155,82,6133,6132,6154,6123,6112,6170,98,105,106,95,6171,101,121,6121,6120,6191,6190,122,6202,6203,6205,141,142,6206,6217,158,6218,163,6215,164,6214,6237,6247,6238,185,186,195,180 
   GROUPA4=VA_H_69-O_6135 GROUPB4=6130,6137,71,73,6160,77,78,79,75,6125,6158,94,6141,100,6145,6143,6144,85,6148,83,6147,99,6162,6164,6163,93,107,90,6152,6150,6151,6115,6172,6113,96,119,117,88,118,103,91,6117,6118,87,102,111,6174,109,6186,6180,113,115,6188,114,6182,6184,6199,6177,6192,6200,6197,6176,135,123,139,6194,6196,133,125,137,150,131,151,156,143,128,147,6207,157,127,154,145,153,6209,148,159,160,161,6221,6227,6212,6219,6224,6211,165,6229,6223,6239,167,170,169,6231,6233,6241,187,6243,6244,6245,193,192,172,191,6235,189,176,173,175,178,179,182,183,181 WEIGHT4=0.5
   GROUPA5=VH_H_107-O_6170 GROUPB5=6190,82,105,122,6154,6205,95,6202,6203,68,6136,142,6206,6135,98,141,101,74,6217,158,6218,163,6123,6124,6215,6214,164,6112,6237,6238,6247,6133,6132,185,6121,186,6120,195,180
   GROUPA6=VA_H_6156-O_81 GROUPB6=119,117,118,6168,83,6167,73,71,6166,77,78,79,94,6137,6147,111,6148,6172,75,90,6174,6150,6152,6151,6164,6163,6162,109,87,88,93,113,115,114,100,6127,91,6129,6130,6192,6180,6186,96,6125,6182,6188,6177,6184,99,6197,6199,123,6176,6200,6115,102,125,103,139,6194,135,6196,137,6113,150,133,131,151,6117,143,147,128,156,6118,127,157,6207,154,145,148,153,6209,6221,159,160,161,6227,6219,6224,6212,165,6229,6211,6223,167,6239,170,169,6233,6231,187,6241,172,193,6244,6243,6245,189,192,6235,191,176,173,175,178,179,182,183,181 WEIGHT6=0.5
   GROUPA7=VH_H_6192-O_121 GROUPB7=6171,141,6190,6206,105,6217,6218,163,6155,82,6202,81,6203,158,164,6215,95,6154,6214,6237,6238,68,101,98,6136,74,6247,185,6135,186,6123,6124,195,6112,180,6133,6132,6121,6120 
   GROUPA8=VH_H_6219-O_163 GROUPB8=6238,6205,6215,6217,6206,6214,186,158,185,141,6237,180,6247,122,6191,195,121,6190,6203,6202,106,6171,6170,105,6155,82,95,81,6154,101,98,6136,68,74,6135,6123,6124,6112,6121,6133,6132,6120 
   GROUPA9=VH_H_143-O_6205 GROUPB9=122,141,158,6215,164,6190,6214,6238,6237,106,6171,6170,6203,6202,6247,185,186,105,6155,82,95,81,195,180,6154,101,98,68,6136,74,6135,6123,6124,6112,6133,6121,6132,6120 
   GROUPA10=VA_H_6192-O_121 GROUPB10=6196,137,123,6199,6200,109,156,6177,6172,87,151,85,6180,147,6207,113,90,6186,154,114,115,127,117,118,119,139,6209,157,128,6160,6163,6164,6156,6158,6162,145,153,91,148,88,131,6219,6221,6182,159,161,160,94,135,6188,6224,96,6141,6212,83,133,6227,93,6184,6211,6139,6143,6168,6167,6166,165,6145,6144,6147,6223,6150,6151,6152,102,167,6239,100,71,6148,170,78,77,79,6229,69,73,6137,103,99,169,75,6233,187,172,6241,6244,6243,6245,176,173,193,6127,6231,192,191,189,175,6235,6115,6125,6129,6130,178,179,6113,183,182,181,6117,6118 WEIGHT10=0.5
   GROUPA11=VA_H_6219-O_163 GROUPB11=153,6221,145,165,6212,172,150,148,6207,161,169,159,156,160,176,127,125,187,147,151,6233,173,6227,157,175,6244,137,6243,6245,6241,6194,6192,128,178,6196,179,6197,6176,193,192,189,123,191,183,182,181,6235,6229,6174,139,6200,6199,131,6177,6231,6180,111,109,107,113,6186,114,115,87,135,6172,133,117,90,118,119,6182,85,91,6188,88,6163,6164,6162,6184,6158,6160,96,6156,94,93,83,6141,102,6143,6145,6144,6150,6151,6152,6166,6168,6167,6147,6139,100,103,6148,71,99,78,77,79,73,6137,69,75,6115,6127,6125,6129,6130,6117,6113,6118 WEIGHT11=0.5
   GROUPA12=VA_H_107-O_6170 GROUPB12=117,119,118,6197,6172,88,6158,94,6199,91,83,6164,6163,6162,6200,113,125,123,115,114,6139,6141,6176,6196,93,6180,137,96,6194,139,6177,6167,6168,6186,6166,6145,6143,6144,71,150,135,143,100,6147,69,78,77,79,131,73,6182,128,133,6150,127,6188,6151,6152,151,156,6148,147,102,75,6207,6137,6184,99,154,157,103,6209,145,6221,148,153,6227,6219,6127,159,160,161,6224,6129,6212,6130,6125,6211,165,6115,6229,6223,6239,167,170,6113,6117,169,6233,6118,6231,6241,6244,6243,187,6245,172,176,6235,173,193,192,189,175,191,178,179,182,183,181 WEIGHT12=0.5
   GROUPA13=VA_HZ1_159-OD2_6215 GROUPB13=6212,156,6207,153,157,6219,6194,150,167,143,151,6239,148,6176,6196,187,6192,6223,6244,6243,6224,6245,125,170,172,147,6221,6197,165,145,6177,6200,137,192,193,191,6174,6199,127,176,173,169,6241,178,6180,189,175,6186,6233,6172,6227,179,139,128,123,183,182,181,107,6163,6164,111,6162,87,90,6182,109,6188,6158,113,131,114,115,91,6235,85,6229,135,96,6160,118,117,6184,119,102,88,133,6156,6231,94,6166,6168,93,6167,6141,103,83,100,6147,6139,6143,6144,6145,6150,6151,6152,99,6148,71,6137,69,78,77,79,73,75,6115,6127,6125,6129,6117,6130,6113,6118 WEIGHT13=0.5
   GROUPA14=VA_H_143-O_6205 GROUPB14=153,148,6224,6197,6207,6194,6221,123,6174,128,6196,6176,157,165,6227,159,161,160,6211,6223,6212,111,107,109,167,6199,6200,139,6177,170,113,6180,6239,131,114,115,87,6186,6172,169,117,118,119,85,90,6233,6229,135,133,172,187,6182,176,91,88,6188,6163,6164,173,6241,6162,6244,6243,6160,6158,6245,175,6156,6184,193,189,96,192,94,191,6235,6231,6141,83,178,93,6143,6145,179,6144,6139,6150,6151,6152,6147,6168,6166,6167,102,182,183,181,100,6148,71,78,77,79,103,73,6137,99,69,75,6127,6115,6125,6129,6130,6113,6117,6118 WEIGHT14=0.5
   SUM
...

NWH_hardF: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_107-O_6170,VA_H_143-O_6205,VA_H_6192-O_121,VA_H_6156-O_81,VA_H_6219-O_163,VA_H_69-O_6135, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH 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=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label NWH_hardF calculates the following quantities: Quantity    Description  
NWH_hardF.value the value of the coordinationNWO_hardF: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_107-O_6170,VH_H_143-O_6205,VH_H_6192-O_121,VH_H_6156-O_81,VH_H_6219-O_163,VH_H_69-O_6135, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label NWO_hardF calculates the following quantities: Quantity    Description  
NWO_hardF.value the value of the coordinationdiffHB_compact_test: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cmapH_sum,NWH_hardF,NWO_hardF,hbnnc_test COEFFICIENTS the coefficients of the arguments in your function=1.0,-0.0625,-0.125,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Now for the side chains 
The COMBINE action with label diffHB_compact_test calculates the following quantities: Quantity    Description  
diffHB_compact_test.value a linear combinationSC6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=72,74,76 MASS calculate the center of mass
The CENTER action with label SC6 calculates the following quantities: Quantity    Description  
SC6.value the position of the center of massSC7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=86,89,92,95,97,98,101 MASS calculate the center of mass
The CENTER action with label SC7 calculates the following quantities: Quantity    Description  
SC7.value the position of the center of massSC8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=110,112,116 MASS calculate the center of mass
The CENTER action with label SC8 calculates the following quantities: Quantity    Description  
SC8.value the position of the center of massSC9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=126,129,130,132,134,136,138 MASS calculate the center of mass
The CENTER action with label SC9 calculates the following quantities: Quantity    Description  
SC9.value the position of the center of massSC10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=146,149,152,155,158 MASS calculate the center of mass
The CENTER action with label SC10 calculates the following quantities: Quantity    Description  
SC10.value the position of the center of massSC11: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=168,171,174,177,180 MASS calculate the center of mass
The CENTER action with label SC11 calculates the following quantities: Quantity    Description  
SC11.value the position of the center of massSC12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=190 MASS calculate the center of mass
The CENTER action with label SC12 calculates the following quantities: Quantity    Description  
SC12.value the position of the center of massSC384: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=6116,6119,6120,6121 MASS calculate the center of mass
The CENTER action with label SC384 calculates the following quantities: Quantity    Description  
SC384.value the position of the center of massSC385: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=6128,6131,6132,6133 MASS calculate the center of mass
The CENTER action with label SC385 calculates the following quantities: Quantity    Description  
SC385.value the position of the center of massSC386: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=6140,6142,6146,6149 MASS calculate the center of mass
The CENTER action with label SC386 calculates the following quantities: Quantity    Description  
SC386.value the position of the center of massSC387: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=6159,6161,6165 MASS calculate the center of mass
The CENTER action with label SC387 calculates the following quantities: Quantity    Description  
SC387.value the position of the center of massSC388: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=6175,6178,6179,6181,6183,6185,6187 MASS calculate the center of mass
The CENTER action with label SC388 calculates the following quantities: Quantity    Description  
SC388.value the position of the center of massSC389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=6195,6198,6201,6202,6203 MASS calculate the center of mass
The CENTER action with label SC389 calculates the following quantities: Quantity    Description  
SC389.value the position of the center of massSC390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=6210,6213,6214,6215 MASS calculate the center of mass
The CENTER action with label SC390 calculates the following quantities: Quantity    Description  
SC390.value the position of the center of massSC391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=6222,6225,6226,6230,6232,6234 MASS calculate the center of mass
The CENTER action with label SC391 calculates the following quantities: Quantity    Description  
SC391.value the position of the center of massSC392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=6242 MASS calculate the center of mass

The CENTER action with label SC392 calculates the following quantities: Quantity    Description  
SC392.value the position of the center of massSC6-8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC8
The CENTER action with label SC6-8 calculates the following quantities: Quantity    Description  
SC6-8.value the position of the center of massSC6-9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC9
The CENTER action with label SC6-9 calculates the following quantities: Quantity    Description  
SC6-9.value the position of the center of massSC6-10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC10
The CENTER action with label SC6-10 calculates the following quantities: Quantity    Description  
SC6-10.value the position of the center of massSC6-11: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC11
The CENTER action with label SC6-11 calculates the following quantities: Quantity    Description  
SC6-11.value the position of the center of massSC6-12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC12
The CENTER action with label SC6-12 calculates the following quantities: Quantity    Description  
SC6-12.value the position of the center of massSC6-384: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC384
The CENTER action with label SC6-384 calculates the following quantities: Quantity    Description  
SC6-384.value the position of the center of massSC6-385: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC385
The CENTER action with label SC6-385 calculates the following quantities: Quantity    Description  
SC6-385.value the position of the center of massSC6-386: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC386
The CENTER action with label SC6-386 calculates the following quantities: Quantity    Description  
SC6-386.value the position of the center of massSC6-387: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC387
The CENTER action with label SC6-387 calculates the following quantities: Quantity    Description  
SC6-387.value the position of the center of massSC6-388: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC388
The CENTER action with label SC6-388 calculates the following quantities: Quantity    Description  
SC6-388.value the position of the center of massSC6-389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC389
The CENTER action with label SC6-389 calculates the following quantities: Quantity    Description  
SC6-389.value the position of the center of massSC6-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC390
The CENTER action with label SC6-390 calculates the following quantities: Quantity    Description  
SC6-390.value the position of the center of massSC6-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC391
The CENTER action with label SC6-391 calculates the following quantities: Quantity    Description  
SC6-391.value the position of the center of massSC6-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC392
The CENTER action with label SC6-392 calculates the following quantities: Quantity    Description  
SC6-392.value the position of the center of massSC7-9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC9
The CENTER action with label SC7-9 calculates the following quantities: Quantity    Description  
SC7-9.value the position of the center of massSC7-10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC10
The CENTER action with label SC7-10 calculates the following quantities: Quantity    Description  
SC7-10.value the position of the center of massSC7-11: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC11
The CENTER action with label SC7-11 calculates the following quantities: Quantity    Description  
SC7-11.value the position of the center of massSC7-12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC12
The CENTER action with label SC7-12 calculates the following quantities: Quantity    Description  
SC7-12.value the position of the center of massSC7-384: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC384
The CENTER action with label SC7-384 calculates the following quantities: Quantity    Description  
SC7-384.value the position of the center of massSC7-385: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC385
The CENTER action with label SC7-385 calculates the following quantities: Quantity    Description  
SC7-385.value the position of the center of massSC7-386: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC386
The CENTER action with label SC7-386 calculates the following quantities: Quantity    Description  
SC7-386.value the position of the center of massSC7-387: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC387
The CENTER action with label SC7-387 calculates the following quantities: Quantity    Description  
SC7-387.value the position of the center of massSC7-388: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC388
The CENTER action with label SC7-388 calculates the following quantities: Quantity    Description  
SC7-388.value the position of the center of massSC7-389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC389
The CENTER action with label SC7-389 calculates the following quantities: Quantity    Description  
SC7-389.value the position of the center of massSC7-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC390
The CENTER action with label SC7-390 calculates the following quantities: Quantity    Description  
SC7-390.value the position of the center of massSC7-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC391
The CENTER action with label SC7-391 calculates the following quantities: Quantity    Description  
SC7-391.value the position of the center of massSC7-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC392
The CENTER action with label SC7-392 calculates the following quantities: Quantity    Description  
SC7-392.value the position of the center of massSC8-10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC10
The CENTER action with label SC8-10 calculates the following quantities: Quantity    Description  
SC8-10.value the position of the center of massSC8-11: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC11
The CENTER action with label SC8-11 calculates the following quantities: Quantity    Description  
SC8-11.value the position of the center of massSC8-12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC12
The CENTER action with label SC8-12 calculates the following quantities: Quantity    Description  
SC8-12.value the position of the center of massSC8-384: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC384
The CENTER action with label SC8-384 calculates the following quantities: Quantity    Description  
SC8-384.value the position of the center of massSC8-385: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC385
The CENTER action with label SC8-385 calculates the following quantities: Quantity    Description  
SC8-385.value the position of the center of massSC8-386: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC386
The CENTER action with label SC8-386 calculates the following quantities: Quantity    Description  
SC8-386.value the position of the center of massSC8-387: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC387
The CENTER action with label SC8-387 calculates the following quantities: Quantity    Description  
SC8-387.value the position of the center of massSC8-388: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC388
The CENTER action with label SC8-388 calculates the following quantities: Quantity    Description  
SC8-388.value the position of the center of massSC8-389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC389
The CENTER action with label SC8-389 calculates the following quantities: Quantity    Description  
SC8-389.value the position of the center of massSC8-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC390
The CENTER action with label SC8-390 calculates the following quantities: Quantity    Description  
SC8-390.value the position of the center of massSC8-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC391
The CENTER action with label SC8-391 calculates the following quantities: Quantity    Description  
SC8-391.value the position of the center of massSC8-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC392
The CENTER action with label SC8-392 calculates the following quantities: Quantity    Description  
SC8-392.value the position of the center of massSC9-11: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC9,SC11
The CENTER action with label SC9-11 calculates the following quantities: Quantity    Description  
SC9-11.value the position of the center of massSC9-12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC9,SC12
The CENTER action with label SC9-12 calculates the following quantities: Quantity    Description  
SC9-12.value the position of the center of massSC9-384: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC9,SC384
The CENTER action with label SC9-384 calculates the following quantities: Quantity    Description  
SC9-384.value the position of the center of massSC9-385: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC9,SC385
The CENTER action with label SC9-385 calculates the following quantities: Quantity    Description  
SC9-385.value the position of the center of massSC9-386: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC9,SC386
The CENTER action with label SC9-386 calculates the following quantities: Quantity    Description  
SC9-386.value the position of the center of massSC9-387: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC9,SC387
The CENTER action with label SC9-387 calculates the following quantities: Quantity    Description  
SC9-387.value the position of the center of massSC9-388: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC9,SC388
The CENTER action with label SC9-388 calculates the following quantities: Quantity    Description  
SC9-388.value the position of the center of massSC9-389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC9,SC389
The CENTER action with label SC9-389 calculates the following quantities: Quantity    Description  
SC9-389.value the position of the center of massSC9-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC9,SC390
The CENTER action with label SC9-390 calculates the following quantities: Quantity    Description  
SC9-390.value the position of the center of massSC9-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC9,SC391
The CENTER action with label SC9-391 calculates the following quantities: Quantity    Description  
SC9-391.value the position of the center of massSC9-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC9,SC392
The CENTER action with label SC9-392 calculates the following quantities: Quantity    Description  
SC9-392.value the position of the center of massSC10-12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC10,SC12
The CENTER action with label SC10-12 calculates the following quantities: Quantity    Description  
SC10-12.value the position of the center of massSC10-384: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC10,SC384
The CENTER action with label SC10-384 calculates the following quantities: Quantity    Description  
SC10-384.value the position of the center of massSC10-385: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC10,SC385
The CENTER action with label SC10-385 calculates the following quantities: Quantity    Description  
SC10-385.value the position of the center of massSC10-386: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC10,SC386
The CENTER action with label SC10-386 calculates the following quantities: Quantity    Description  
SC10-386.value the position of the center of massSC10-387: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC10,SC387
The CENTER action with label SC10-387 calculates the following quantities: Quantity    Description  
SC10-387.value the position of the center of massSC10-388: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC10,SC388
The CENTER action with label SC10-388 calculates the following quantities: Quantity    Description  
SC10-388.value the position of the center of massSC10-389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC10,SC389
The CENTER action with label SC10-389 calculates the following quantities: Quantity    Description  
SC10-389.value the position of the center of massSC10-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC10,SC390
The CENTER action with label SC10-390 calculates the following quantities: Quantity    Description  
SC10-390.value the position of the center of massSC10-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC10,SC391
The CENTER action with label SC10-391 calculates the following quantities: Quantity    Description  
SC10-391.value the position of the center of massSC10-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC10,SC392
The CENTER action with label SC10-392 calculates the following quantities: Quantity    Description  
SC10-392.value the position of the center of massSC11-384: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC11,SC384
The CENTER action with label SC11-384 calculates the following quantities: Quantity    Description  
SC11-384.value the position of the center of massSC11-385: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC11,SC385
The CENTER action with label SC11-385 calculates the following quantities: Quantity    Description  
SC11-385.value the position of the center of massSC11-386: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC11,SC386
The CENTER action with label SC11-386 calculates the following quantities: Quantity    Description  
SC11-386.value the position of the center of massSC11-387: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC11,SC387
The CENTER action with label SC11-387 calculates the following quantities: Quantity    Description  
SC11-387.value the position of the center of massSC11-388: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC11,SC388
The CENTER action with label SC11-388 calculates the following quantities: Quantity    Description  
SC11-388.value the position of the center of massSC11-389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC11,SC389
The CENTER action with label SC11-389 calculates the following quantities: Quantity    Description  
SC11-389.value the position of the center of massSC11-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC11,SC390
The CENTER action with label SC11-390 calculates the following quantities: Quantity    Description  
SC11-390.value the position of the center of massSC11-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC11,SC391
The CENTER action with label SC11-391 calculates the following quantities: Quantity    Description  
SC11-391.value the position of the center of massSC11-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC11,SC392
The CENTER action with label SC11-392 calculates the following quantities: Quantity    Description  
SC11-392.value the position of the center of massSC12-384: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC12,SC384
The CENTER action with label SC12-384 calculates the following quantities: Quantity    Description  
SC12-384.value the position of the center of massSC12-385: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC12,SC385
The CENTER action with label SC12-385 calculates the following quantities: Quantity    Description  
SC12-385.value the position of the center of massSC12-386: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC12,SC386
The CENTER action with label SC12-386 calculates the following quantities: Quantity    Description  
SC12-386.value the position of the center of massSC12-387: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC12,SC387
The CENTER action with label SC12-387 calculates the following quantities: Quantity    Description  
SC12-387.value the position of the center of massSC12-388: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC12,SC388
The CENTER action with label SC12-388 calculates the following quantities: Quantity    Description  
SC12-388.value the position of the center of massSC12-389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC12,SC389
The CENTER action with label SC12-389 calculates the following quantities: Quantity    Description  
SC12-389.value the position of the center of massSC12-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC12,SC390
The CENTER action with label SC12-390 calculates the following quantities: Quantity    Description  
SC12-390.value the position of the center of massSC12-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC12,SC391
The CENTER action with label SC12-391 calculates the following quantities: Quantity    Description  
SC12-391.value the position of the center of massSC12-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC12,SC392
The CENTER action with label SC12-392 calculates the following quantities: Quantity    Description  
SC12-392.value the position of the center of massSC384-386: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC384,SC386
The CENTER action with label SC384-386 calculates the following quantities: Quantity    Description  
SC384-386.value the position of the center of massSC384-387: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC384,SC387
The CENTER action with label SC384-387 calculates the following quantities: Quantity    Description  
SC384-387.value the position of the center of massSC384-388: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC384,SC388
The CENTER action with label SC384-388 calculates the following quantities: Quantity    Description  
SC384-388.value the position of the center of massSC384-389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC384,SC389
The CENTER action with label SC384-389 calculates the following quantities: Quantity    Description  
SC384-389.value the position of the center of massSC384-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC384,SC390
The CENTER action with label SC384-390 calculates the following quantities: Quantity    Description  
SC384-390.value the position of the center of massSC384-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC384,SC391
The CENTER action with label SC384-391 calculates the following quantities: Quantity    Description  
SC384-391.value the position of the center of massSC384-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC384,SC392
The CENTER action with label SC384-392 calculates the following quantities: Quantity    Description  
SC384-392.value the position of the center of massSC385-387: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC385,SC387
The CENTER action with label SC385-387 calculates the following quantities: Quantity    Description  
SC385-387.value the position of the center of massSC385-388: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC385,SC388
The CENTER action with label SC385-388 calculates the following quantities: Quantity    Description  
SC385-388.value the position of the center of massSC385-389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC385,SC389
The CENTER action with label SC385-389 calculates the following quantities: Quantity    Description  
SC385-389.value the position of the center of massSC385-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC385,SC390
The CENTER action with label SC385-390 calculates the following quantities: Quantity    Description  
SC385-390.value the position of the center of massSC385-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC385,SC391
The CENTER action with label SC385-391 calculates the following quantities: Quantity    Description  
SC385-391.value the position of the center of massSC385-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC385,SC392
The CENTER action with label SC385-392 calculates the following quantities: Quantity    Description  
SC385-392.value the position of the center of massSC386-388: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC386,SC388
The CENTER action with label SC386-388 calculates the following quantities: Quantity    Description  
SC386-388.value the position of the center of massSC386-389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC386,SC389
The CENTER action with label SC386-389 calculates the following quantities: Quantity    Description  
SC386-389.value the position of the center of massSC386-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC386,SC390
The CENTER action with label SC386-390 calculates the following quantities: Quantity    Description  
SC386-390.value the position of the center of massSC386-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC386,SC391
The CENTER action with label SC386-391 calculates the following quantities: Quantity    Description  
SC386-391.value the position of the center of massSC386-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC386,SC392
The CENTER action with label SC386-392 calculates the following quantities: Quantity    Description  
SC386-392.value the position of the center of massSC387-389: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC387,SC389
The CENTER action with label SC387-389 calculates the following quantities: Quantity    Description  
SC387-389.value the position of the center of massSC387-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC387,SC390
The CENTER action with label SC387-390 calculates the following quantities: Quantity    Description  
SC387-390.value the position of the center of massSC387-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC387,SC391
The CENTER action with label SC387-391 calculates the following quantities: Quantity    Description  
SC387-391.value the position of the center of massSC387-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC387,SC392
The CENTER action with label SC387-392 calculates the following quantities: Quantity    Description  
SC387-392.value the position of the center of massSC388-390: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC388,SC390
The CENTER action with label SC388-390 calculates the following quantities: Quantity    Description  
SC388-390.value the position of the center of massSC388-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC388,SC391
The CENTER action with label SC388-391 calculates the following quantities: Quantity    Description  
SC388-391.value the position of the center of massSC388-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC388,SC392
The CENTER action with label SC388-392 calculates the following quantities: Quantity    Description  
SC388-392.value the position of the center of massSC389-391: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC389,SC391
The CENTER action with label SC389-391 calculates the following quantities: Quantity    Description  
SC389-391.value the position of the center of massSC389-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC389,SC392
The CENTER action with label SC389-392 calculates the following quantities: Quantity    Description  
SC389-392.value the position of the center of massSC390-392: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC390,SC392

The CENTER action with label SC390-392 calculates the following quantities: Quantity    Description  
SC390-392.value the position of the center of masscontsideF: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC6,SC7,SC7,SC8,SC8,SC9,SC9,SC10,SC10,SC11,SC11, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC386,SC387,SC389,SC386,SC388,SC389,SC391,SC388,SC390,SC391,SC392, 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=4 MM=6} PAIR Pair only 1st element of the 1st group with 1st element in the second, etc
The COORDINATION action with label contsideF calculates the following quantities: Quantity    Description  
contsideF.value the value of the coordinationcoormap_sum: COORDINATIONMAPThis action is not part of PLUMED and was included by using a LOAD command More details ...
   GROUPA1=SC6-386 GROUPB1=SC7,SC8,SC9,SC10,SC11,SC12,SC384,SC385,SC387,SC388,SC389,SC390,SC391,SC392 SWITCH1={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5}
   GROUPA2=SC7-387 GROUPB2=SC6,SC8,SC9,SC10,SC11,SC12,SC384,SC385,SC386,SC388,SC389,SC390,SC391,SC392
   GROUPA3=SC7-389 GROUPB3=SC6,SC8,SC9,SC10,SC11,SC12,SC384,SC385,SC386,SC387,SC388,SC390,SC391,SC392
   GROUPA4=SC8-386 GROUPB4=SC6,SC7,SC9,SC10,SC11,SC12,SC384,SC385,SC387,SC388,SC389,SC390,SC391,SC392
   GROUPA5=SC8-388 GROUPB5=SC6,SC7,SC9,SC10,SC11,SC12,SC384,SC385,SC386,SC387,SC389,SC390,SC391,SC392
   GROUPA6=SC9-389 GROUPB6=SC6,SC7,SC8,SC10,SC11,SC12,SC384,SC385,SC386,SC387,SC388,SC390,SC391,SC392
   GROUPA7=SC9-391 GROUPB7=SC6,SC7,SC8,SC10,SC11,SC12,SC384,SC385,SC386,SC387,SC388,SC389,SC390,SC392
   GROUPA8=SC10-388 GROUPB8=SC6,SC7,SC8,SC9,SC11,SC12,SC384,SC385,SC386,SC387,SC389,SC390,SC391,SC392
   GROUPA9=SC10-390 GROUPB9=SC6,SC7,SC8,SC9,SC11,SC12,SC384,SC385,SC386,SC387,SC388,SC389,SC391,SC392
   GROUPA10=SC11-391 GROUPB10=SC6,SC7,SC8,SC9,SC10,SC12,SC384,SC385,SC386,SC387,SC388,SC389,SC390,SC392
   GROUPA11=SC11-392 GROUPB11=SC6,SC7,SC8,SC9,SC10,SC12,SC384,SC385,SC386,SC387,SC388,SC389,SC390,SC391
   SUM
...
cmap_compact_test: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contsideF,coormap_sum COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The COMBINE action with label cmap_compact_test calculates the following quantities: Quantity    Description  
cmap_compact_test.value a linear combinationC6149: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=6149 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label C6149 calculates the following quantities: Quantity    Description  
C6149.value the value of the coordinationC6228: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=6228 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label C6228 calculates the following quantities: Quantity    Description  
C6228.value the value of the coordinationC6226: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=6226 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label C6226 calculates the following quantities: Quantity    Description  
C6226.value the value of the coordinationC6230: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=6230 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label C6230 calculates the following quantities: Quantity    Description  
C6230.value the value of the coordinationO121: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=121 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label O121 calculates the following quantities: Quantity    Description  
O121.value the value of the coordinationO6170: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=6170 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label O6170 calculates the following quantities: Quantity    Description  
O6170.value the value of the coordinationO6205: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=6205 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20

# --- Beta strand 1 --- (centers of heavy sidechain atoms) +2
The COORDINATION action with label O6205 calculates the following quantities: Quantity    Description  
O6205.value the value of the coordinationbeta1_grp: 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=SC6,SC7,SC8,SC9,SC10,SC11,SC12

# --- Beta strand 20 --- (centers of heavy sidechain atoms) +2 +2
The GROUP action with label beta1_grp calculates somethingbeta20_grp: 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=SC384,SC385,SC386,SC387,SC388,SC389,SC390,SC391,SC392

# --- Other beta strands (1–19) --- (C-alpha atoms only)
The GROUP action with label beta20_grp calculates somethingbeta_1_19_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=70,84,108,124,144,166,188,266,285,299,315,336,408,420,440,456,565,577,593,605,612,628,644,663,821,845,861,882,898,912,931,945,956,966,986,1010,1195,1215,1239,1261,1273,1292,1312,1328,1338,1352,1368,1385,1396,1825,1835,1858,1870,1890,1904,1924,2055,2071,2085,2104,2236,2247,2254,2270,2282,2303,2318,2334,2356,2366,2386,2405,2611,2622,2638,2662,2681,2697,2716,2740,2762,2778,2969,2984,2998,3012,3036,3168,3187,3204,3223,3238,3248,3259,3327,3346,3367,3441,3460,3471,3487,3501,3517,3534,3550,3564,3656,3672,3694,3716,3735,3757,3776,3787,3803,3827,3844,3865,3875,3887,3999,4016,4037,4059,4077,4089,4105,4115,4132,4147,4162,4261,4272,4286,4306,4317,4339,4355,4376,4390,4606,4625,4635,5065,5084,5103,5119,5130,5151,5173,5189,5211,5227,5249,5268,5284,5446,5457,5469,5485,5495,5511,5526,5547,5559,5579,5593,5612

# --- C-tail and Gate Loop --- (C-alpha atoms only) 
The GROUP action with label beta_1_19_ca calculates somethingCtail_ca_grp: 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=6220,6240,6250,6274,6291,6315
The GROUP action with label Ctail_ca_grp calculates somethingGateLoop_ca_grp: 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=4654,4666,4673,4695,4714,4736,4753,4768,4780,4794,4808


# --- CENTER ATOMS
The GROUP action with label GateLoop_ca_grp calculates somethingbeta1CTR: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=beta1_grp
The CENTER action with label beta1CTR calculates the following quantities: Quantity    Description  
beta1CTR.value the position of the center of massbeta20CTR: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=beta20_grp
The CENTER action with label beta20CTR calculates the following quantities: Quantity    Description  
beta20CTR.value the position of the center of massbeta_1_19_caCTR: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=beta_1_19_ca

The CENTER action with label beta_1_19_caCTR calculates the following quantities: Quantity    Description  
beta_1_19_caCTR.value the position of the center of massCtailCTR: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=Ctail_ca_grp
The CENTER action with label CtailCTR calculates the following quantities: Quantity    Description  
CtailCTR.value the position of the center of massGateLoopCTR: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=GateLoop_ca_grp


# --- CVs DEFINITION
# --- CV1: number of contacts between beta1 and beta20 ---
The CENTER action with label GateLoopCTR calculates the following quantities: Quantity    Description  
GateLoopCTR.value the position of the center of massc1_20: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=beta1_grp GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=beta20_grp 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 R_0=0.40 NN=6 MM=12} #NLIST=nl

# --- CV2: number of contacts between beta20 and all other beta strands (1–19) ---
The COORDINATION action with label c1_20 calculates the following quantities: Quantity    Description  
c1_20.value the value of the coordinationc20_others: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=beta20_grp GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=beta_1_19_ca 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 R_0=0.45 NN=6 MM=12} #NLIST=nl

# --- CV3: distance between C-terminus and gate loop --- 
The COORDINATION action with label c20_others calculates the following quantities: Quantity    Description  
c20_others.value the value of the coordinationd_ct_gl_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=CtailCTR,GateLoopCTR

# --- CV4: distance between beta20 and all other beta strands (1–19) ---
The DISTANCE action with label d_ct_gl_dist calculates the following quantities: Quantity    Description  
d_ct_gl_dist.value the DISTANCE between this pair of atomsd_20_others_dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta20CTR,beta_1_19_caCTR

# --- Attempt of cylidric constraint ---
The DISTANCE action with label d_20_others_dist calculates the following quantities: Quantity    Description  
d_20_others_dist.value the DISTANCE between this pair of atomslig: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=6114,6126,6138,6157,6173,6193,6208,6220,6240
The CENTER action with label lig calculates the following quantities: Quantity    Description  
lig.value the position of the center of massp0: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1181,1195,1215,1239,1261
The CENTER action with label p0 calculates the following quantities: Quantity    Description  
p0.value the position of the center of massp1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=108,124,144,166,188
The CENTER action with label p1 calculates the following quantities: Quantity    Description  
p1.value the position of the center of masspp: PROJECTION_ON_AXISCalculate a position based on the projection along and extension from a defined axis. More details AXIS_ATOMSThe atoms that define the direction of the axis of interest=p0,p1 ATOMThe atom whose position we want to project on the axis of interest=lig

The PROJECTION_ON_AXIS action with label pp calculates the following quantities: Quantity    Description  
pp.value the value of the projection along the axisuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.ext ATthe positions of the wall=1.5 KAPPAthe force constant for the wall=5000 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0

The UPPER_WALLS action with label uwall calculates the following quantities: Quantity    Description  
uwall.bias the instantaneous value of the bias potential
uwall.force2 the instantaneous value of the squared force due to this bias potentialr: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../npt_300_elongated_soloCA_beta_1_19.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
The RMSD action with label r calculates the following quantities: Quantity    Description  
r.value the RMSD distance between the instantaneous structure and the reference structure/s that were inputuwall_rmsd: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=r ATthe positions of the wall=0.05 KAPPAthe force constant for the wall=50000 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0

The UPPER_WALLS action with label uwall_rmsd calculates the following quantities: Quantity    Description  
uwall_rmsd.bias the instantaneous value of the bias potential
uwall_rmsd.force2 the instantaneous value of the squared force due to this bias potentiallwall_d_20_others_dist: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d_20_others_dist ATthe positions of the wall=2.5 KAPPAthe force constant for the wall=5000 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0
The LOWER_WALLS action with label lwall_d_20_others_dist calculates the following quantities: Quantity    Description  
lwall_d_20_others_dist.bias the instantaneous value of the bias potential
lwall_d_20_others_dist.force2 the instantaneous value of the squared force due to this bias potentialuwall_proj: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.proj ATthe positions of the wall=5.5 KAPPAthe force constant for the wall=5000 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0

The UPPER_WALLS action with label uwall_proj calculates the following quantities: Quantity    Description  
uwall_proj.bias the instantaneous value of the bias potential
uwall_proj.force2 the instantaneous value of the squared force due to this bias potentialfSC_proj: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cmap_compact_test,pp.proj FUNCthe function you wish to evaluate=y-4.168+0.1143*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label fSC_proj calculates the following quantities: Quantity    Description  
fSC_proj.value an arbitrary functionlwallfSC_proj: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=fSC_proj ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=500.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0

The LOWER_WALLS action with label lwallfSC_proj calculates the following quantities: Quantity    Description  
lwallfSC_proj.bias the instantaneous value of the bias potential
lwallfSC_proj.force2 the instantaneous value of the squared force due to this bias potentialfHB_proj: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=diffHB_compact_test,pp.proj FUNCthe function you wish to evaluate=y-2.914+0.08937*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label fHB_proj calculates the following quantities: Quantity    Description  
fHB_proj.value an arbitrary functionlwallfHB_proj: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=fHB_proj ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=500.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0

# Hydration CVs
The LOWER_WALLS action with label lwallfHB_proj calculates the following quantities: Quantity    Description  
lwallfHB_proj.bias the instantaneous value of the bias potential
lwallfHB_proj.force2 the instantaneous value of the squared force due to this bias potentialhyd8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=121 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.35 NN=6 MM=10 D_MAX=1.20} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label hyd8 calculates the following quantities: Quantity    Description  
hyd8.value the value of the coordinationhyd9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=141 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.35 NN=6 MM=10 D_MAX=1.20} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label hyd9 calculates the following quantities: Quantity    Description  
hyd9.value the value of the coordinationhyd10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=162 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.35 NN=6 MM=10 D_MAX=1.20} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label hyd10 calculates the following quantities: Quantity    Description  
hyd10.value the value of the coordinationhyd11: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=185 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.35 NN=6 MM=10 D_MAX=1.20} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label hyd11 calculates the following quantities: Quantity    Description  
hyd11.value the value of the coordinationhyd12: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=194 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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=0.35 NN=6 MM=10 D_MAX=1.20} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20

The COORDINATION action with label hyd12 calculates the following quantities: Quantity    Description  
hyd12.value the value of the coordinationOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=opes
	ARGthe labels of the scalars on which the bias will act (a vector must have a single element, e=diffHB_compact_test,cmap_compact_test,d_20_others_dist
	SIGMA the initial widths of the kernels, divided by the square root of gamma=0.71,0.26,0.67
	FILE a file in which the list of all deposited kernels is stored=Kernels.data
	STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
	STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
	PACEthe frequency for kernel deposition=10000
	#RESTART=YES
	BARRIERthe free energy barrier to be overcome=75.0
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opes calculates the following quantities: Quantity    Description  
opes.bias the instantaneous value of the bias potential
opes.rct estimate of c(t)
opes.zed estimate of Z_n
opes.neff effective sample size
opes.nker total number of compressed kernels used to represent the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=opeshyd12
	ARGthe labels of the scalars on which the bias will act (a vector must have a single element, e=hyd12
	SIGMA the initial widths of the kernels, divided by the square root of gamma=0.42
	FILE a file in which the list of all deposited kernels is stored=Kernelshyd12.data
	STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelshyd12
	STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelshyd12
	PACEthe frequency for kernel deposition=20000
	#RESTART=YES
	BARRIERthe free energy barrier to be overcome=4.0
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opeshyd12 calculates the following quantities: Quantity    Description  
opeshyd12.bias the instantaneous value of the bias potential
opeshyd12.rct estimate of c(t)
opeshyd12.zed estimate of Z_n
opeshyd12.neff effective sample size
opeshyd12.nker total number of compressed kernels used to represent the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=opeshyd11
	ARGthe labels of the scalars on which the bias will act (a vector must have a single element, e=hyd11
	SIGMA the initial widths of the kernels, divided by the square root of gamma=0.27
	FILE a file in which the list of all deposited kernels is stored=Kernelshyd11.data
	STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelshyd11
	STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelshyd11
	PACEthe frequency for kernel deposition=20000
	#RESTART=YES
	BARRIERthe free energy barrier to be overcome=4.0
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opeshyd11 calculates the following quantities: Quantity    Description  
opeshyd11.bias the instantaneous value of the bias potential
opeshyd11.rct estimate of c(t)
opeshyd11.zed estimate of Z_n
opeshyd11.neff effective sample size
opeshyd11.nker total number of compressed kernels used to represent the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=opeshyd10
	ARGthe labels of the scalars on which the bias will act (a vector must have a single element, e=hyd10
	SIGMA the initial widths of the kernels, divided by the square root of gamma=0.59
	FILE a file in which the list of all deposited kernels is stored=Kernelshyd10.data
	STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelshyd10
	STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelshyd10
	PACEthe frequency for kernel deposition=20000
	#RESTART=YES
	BARRIERthe free energy barrier to be overcome=4.0
... OPES_METAD_EXPLORE


The OPES_METAD_EXPLORE action with label opeshyd10 calculates the following quantities: Quantity    Description  
opeshyd10.bias the instantaneous value of the bias potential
opeshyd10.rct estimate of c(t)
opeshyd10.zed estimate of Z_n
opeshyd10.neff effective sample size
opeshyd10.nker total number of compressed kernels used to represent the biasene: ENERGYCalculate the total potential energy of the simulation box. More details


The ENERGY action with label ene calculates somethingPRINTPrint 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=opes.bias,ene,rmsd_ca,diffHB_compact_test,cmap_compact_test,c1_20,c20_others,d_ct_gl_dist,d_20_others_dist,pp.proj,pp.ext,uwall.bias,r,uwall_rmsd.bias,lwall_d_20_others_dist.bias,uwall_proj.bias,fSC_proj,lwallfSC_proj.bias,fHB_proj,lwallfHB_proj.bias,hyd8,hyd9,hyd10,hyd11,hyd12,opeshyd12.bias,opeshyd11.bias,opeshyd10.bias FILEthe name of the file on which to output these quantities=COLVAR
Quantity	Description
rmsd_ca.value	the RMSD distance between the instantaneous structure and the reference structure/s that were input
Quantity	Description
NWH_hardF.value	the value of the coordination
Quantity	Description
NWO_hardF.value	the value of the coordination
Quantity	Description
diffHB_compact_test.value	a linear combination
Quantity	Description
SC6.value	the position of the center of mass
Quantity	Description
SC7.value	the position of the center of mass
Quantity	Description
SC8.value	the position of the center of mass
Quantity	Description
SC9.value	the position of the center of mass
Quantity	Description
SC10.value	the position of the center of mass
Quantity	Description
SC11.value	the position of the center of mass
Quantity	Description
SC12.value	the position of the center of mass
Quantity	Description
SC384.value	the position of the center of mass
Quantity	Description
SC385.value	the position of the center of mass
Quantity	Description
SC386.value	the position of the center of mass
Quantity	Description
SC387.value	the position of the center of mass
Quantity	Description
SC388.value	the position of the center of mass
Quantity	Description
SC389.value	the position of the center of mass
Quantity	Description
SC390.value	the position of the center of mass
Quantity	Description
SC391.value	the position of the center of mass
Quantity	Description
SC392.value	the position of the center of mass
PLUMED-NEST

The public repository of the PLUMED consortium
