PLUMED-NEST

Project ID: plumID:20.016
Source: Naphthalene/plumed.dat
Originally used with PLUMED version: 2.6-dev
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 simulation. This command will append results of new simulations to the same output files, e.g. COLVAR.
# RESTART

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=PairOrientationalEntropy.cpp
The LOAD action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=PairOrientationalEntropyPerpendicular.cpp

# Define groups for the CV
C8: 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=8-648:18 # Head
The GROUP action with label C8 calculates somethingC9: 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=9-648:18 # Head
The GROUP action with label C9 calculates somethingINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=centers.dat
# The command:
# INCLUDE FILE=centers.dat
# ensures PLUMED loads the contents of the file called centers.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label centers.dat calculates somethingstart1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,2
The CENTER action with label start1 calculates the following quantities:
 Quantity   
 Description  
start1.value
the position of the center of massstart2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=19,20
The CENTER action with label start2 calculates the following quantities:
 Quantity   
 Description  
start2.value
the position of the center of massstart3: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=37,38
The CENTER action with label start3 calculates the following quantities:
 Quantity   
 Description  
start3.value
the position of the center of massstart4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=55,56
The CENTER action with label start4 calculates the following quantities:
 Quantity   
 Description  
start4.value
the position of the center of massstart5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=73,74
The CENTER action with label start5 calculates the following quantities:
 Quantity   
 Description  
start5.value
the position of the center of massstart6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=91,92
The CENTER action with label start6 calculates the following quantities:
 Quantity   
 Description  
start6.value
the position of the center of massstart7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=109,110
The CENTER action with label start7 calculates the following quantities:
 Quantity   
 Description  
start7.value
the position of the center of massstart8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=127,128
The CENTER action with label start8 calculates the following quantities:
 Quantity   
 Description  
start8.value
the position of the center of massstart9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=145,146
The CENTER action with label start9 calculates the following quantities:
 Quantity   
 Description  
start9.value
the position of the center of massstart10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=163,164
The CENTER action with label start10 calculates the following quantities:
 Quantity   
 Description  
start10.value
the position of the center of massstart11: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=181,182
The CENTER action with label start11 calculates the following quantities:
 Quantity   
 Description  
start11.value
the position of the center of massstart12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=199,200
The CENTER action with label start12 calculates the following quantities:
 Quantity   
 Description  
start12.value
the position of the center of massstart13: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=217,218
The CENTER action with label start13 calculates the following quantities:
 Quantity   
 Description  
start13.value
the position of the center of massstart14: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=235,236
The CENTER action with label start14 calculates the following quantities:
 Quantity   
 Description  
start14.value
the position of the center of massstart15: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=253,254
The CENTER action with label start15 calculates the following quantities:
 Quantity   
 Description  
start15.value
the position of the center of massstart16: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=271,272
The CENTER action with label start16 calculates the following quantities:
 Quantity   
 Description  
start16.value
the position of the center of massstart17: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=289,290
The CENTER action with label start17 calculates the following quantities:
 Quantity   
 Description  
start17.value
the position of the center of massstart18: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=307,308
The CENTER action with label start18 calculates the following quantities:
 Quantity   
 Description  
start18.value
the position of the center of massstart19: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=325,326
The CENTER action with label start19 calculates the following quantities:
 Quantity   
 Description  
start19.value
the position of the center of massstart20: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=343,344
The CENTER action with label start20 calculates the following quantities:
 Quantity   
 Description  
start20.value
the position of the center of massstart21: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=361,362
The CENTER action with label start21 calculates the following quantities:
 Quantity   
 Description  
start21.value
the position of the center of massstart22: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=379,380
The CENTER action with label start22 calculates the following quantities:
 Quantity   
 Description  
start22.value
the position of the center of massstart23: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=397,398
The CENTER action with label start23 calculates the following quantities:
 Quantity   
 Description  
start23.value
the position of the center of massstart24: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=415,416
The CENTER action with label start24 calculates the following quantities:
 Quantity   
 Description  
start24.value
the position of the center of massstart25: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=433,434
The CENTER action with label start25 calculates the following quantities:
 Quantity   
 Description  
start25.value
the position of the center of massstart26: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=451,452
The CENTER action with label start26 calculates the following quantities:
 Quantity   
 Description  
start26.value
the position of the center of massstart27: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=469,470
The CENTER action with label start27 calculates the following quantities:
 Quantity   
 Description  
start27.value
the position of the center of massstart28: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=487,488
The CENTER action with label start28 calculates the following quantities:
 Quantity   
 Description  
start28.value
the position of the center of massstart29: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=505,506
The CENTER action with label start29 calculates the following quantities:
 Quantity   
 Description  
start29.value
the position of the center of massstart30: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=523,524
The CENTER action with label start30 calculates the following quantities:
 Quantity   
 Description  
start30.value
the position of the center of massstart31: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=541,542
The CENTER action with label start31 calculates the following quantities:
 Quantity   
 Description  
start31.value
the position of the center of massstart32: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=559,560
The CENTER action with label start32 calculates the following quantities:
 Quantity   
 Description  
start32.value
the position of the center of massstart33: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=577,578
The CENTER action with label start33 calculates the following quantities:
 Quantity   
 Description  
start33.value
the position of the center of massstart34: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=595,596
The CENTER action with label start34 calculates the following quantities:
 Quantity   
 Description  
start34.value
the position of the center of massstart35: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=613,614
The CENTER action with label start35 calculates the following quantities:
 Quantity   
 Description  
start35.value
the position of the center of massstart36: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=631,632
The CENTER action with label start36 calculates the following quantities:
 Quantity   
 Description  
start36.value
the position of the center of massSTARTS: 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=start1,start2,start3,start4,start5,start6,start7,start8,start9,start10,start11,start12,start13,start14,start15,start16,start17,start18,start19,start20,start21,start22,start23,start24,start25,start26,start27,start28,start29,start30,start31,start32,start33,start34,start35,start36
The GROUP action with label STARTS calculates somethingend1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=5,7
The CENTER action with label end1 calculates the following quantities:
 Quantity   
 Description  
end1.value
the position of the center of massend2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=23,25
The CENTER action with label end2 calculates the following quantities:
 Quantity   
 Description  
end2.value
the position of the center of massend3: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=41,43
The CENTER action with label end3 calculates the following quantities:
 Quantity   
 Description  
end3.value
the position of the center of massend4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=59,61
The CENTER action with label end4 calculates the following quantities:
 Quantity   
 Description  
end4.value
the position of the center of massend5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=77,79
The CENTER action with label end5 calculates the following quantities:
 Quantity   
 Description  
end5.value
the position of the center of massend6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=95,97
The CENTER action with label end6 calculates the following quantities:
 Quantity   
 Description  
end6.value
the position of the center of massend7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=113,115
The CENTER action with label end7 calculates the following quantities:
 Quantity   
 Description  
end7.value
the position of the center of massend8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=131,133
The CENTER action with label end8 calculates the following quantities:
 Quantity   
 Description  
end8.value
the position of the center of massend9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=149,151
The CENTER action with label end9 calculates the following quantities:
 Quantity   
 Description  
end9.value
the position of the center of massend10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=167,169
The CENTER action with label end10 calculates the following quantities:
 Quantity   
 Description  
end10.value
the position of the center of massend11: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=185,187
The CENTER action with label end11 calculates the following quantities:
 Quantity   
 Description  
end11.value
the position of the center of massend12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=203,205
The CENTER action with label end12 calculates the following quantities:
 Quantity   
 Description  
end12.value
the position of the center of massend13: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=221,223
The CENTER action with label end13 calculates the following quantities:
 Quantity   
 Description  
end13.value
the position of the center of massend14: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=239,241
The CENTER action with label end14 calculates the following quantities:
 Quantity   
 Description  
end14.value
the position of the center of massend15: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=257,259
The CENTER action with label end15 calculates the following quantities:
 Quantity   
 Description  
end15.value
the position of the center of massend16: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=275,277
The CENTER action with label end16 calculates the following quantities:
 Quantity   
 Description  
end16.value
the position of the center of massend17: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=293,295
The CENTER action with label end17 calculates the following quantities:
 Quantity   
 Description  
end17.value
the position of the center of massend18: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=311,313
The CENTER action with label end18 calculates the following quantities:
 Quantity   
 Description  
end18.value
the position of the center of massend19: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=329,331
The CENTER action with label end19 calculates the following quantities:
 Quantity   
 Description  
end19.value
the position of the center of massend20: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=347,349
The CENTER action with label end20 calculates the following quantities:
 Quantity   
 Description  
end20.value
the position of the center of massend21: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=365,367
The CENTER action with label end21 calculates the following quantities:
 Quantity   
 Description  
end21.value
the position of the center of massend22: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=383,385
The CENTER action with label end22 calculates the following quantities:
 Quantity   
 Description  
end22.value
the position of the center of massend23: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=401,403
The CENTER action with label end23 calculates the following quantities:
 Quantity   
 Description  
end23.value
the position of the center of massend24: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=419,421
The CENTER action with label end24 calculates the following quantities:
 Quantity   
 Description  
end24.value
the position of the center of massend25: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=437,439
The CENTER action with label end25 calculates the following quantities:
 Quantity   
 Description  
end25.value
the position of the center of massend26: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=455,457
The CENTER action with label end26 calculates the following quantities:
 Quantity   
 Description  
end26.value
the position of the center of massend27: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=473,475
The CENTER action with label end27 calculates the following quantities:
 Quantity   
 Description  
end27.value
the position of the center of massend28: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=491,493
The CENTER action with label end28 calculates the following quantities:
 Quantity   
 Description  
end28.value
the position of the center of massend29: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=509,511
The CENTER action with label end29 calculates the following quantities:
 Quantity   
 Description  
end29.value
the position of the center of massend30: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=527,529
The CENTER action with label end30 calculates the following quantities:
 Quantity   
 Description  
end30.value
the position of the center of massend31: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=545,547
The CENTER action with label end31 calculates the following quantities:
 Quantity   
 Description  
end31.value
the position of the center of massend32: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=563,565
The CENTER action with label end32 calculates the following quantities:
 Quantity   
 Description  
end32.value
the position of the center of massend33: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=581,583
The CENTER action with label end33 calculates the following quantities:
 Quantity   
 Description  
end33.value
the position of the center of massend34: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=599,601
The CENTER action with label end34 calculates the following quantities:
 Quantity   
 Description  
end34.value
the position of the center of massend35: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=617,619
The CENTER action with label end35 calculates the following quantities:
 Quantity   
 Description  
end35.value
the position of the center of massend36: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=635,637
The CENTER action with label end36 calculates the following quantities:
 Quantity   
 Description  
end36.value
the position of the center of massENDS: 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=end1,end2,end3,end4,end5,end6,end7,end8,end9,end10,end11,end12,end13,end14,end15,end16,end17,end18,end19,end20,end21,end22,end23,end24,end25,end26,end27,end28,end29,end30,end31,end32,end33,end34,end35,end36
The GROUP action with label ENDS calculates somethingcenter1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=8,9
The CENTER action with label center1 calculates the following quantities:
 Quantity   
 Description  
center1.value
the position of the center of masscenter2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=26,27
The CENTER action with label center2 calculates the following quantities:
 Quantity   
 Description  
center2.value
the position of the center of masscenter3: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=44,45
The CENTER action with label center3 calculates the following quantities:
 Quantity   
 Description  
center3.value
the position of the center of masscenter4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=62,63
The CENTER action with label center4 calculates the following quantities:
 Quantity   
 Description  
center4.value
the position of the center of masscenter5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=80,81
The CENTER action with label center5 calculates the following quantities:
 Quantity   
 Description  
center5.value
the position of the center of masscenter6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=98,99
The CENTER action with label center6 calculates the following quantities:
 Quantity   
 Description  
center6.value
the position of the center of masscenter7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=116,117
The CENTER action with label center7 calculates the following quantities:
 Quantity   
 Description  
center7.value
the position of the center of masscenter8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=134,135
The CENTER action with label center8 calculates the following quantities:
 Quantity   
 Description  
center8.value
the position of the center of masscenter9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=152,153
The CENTER action with label center9 calculates the following quantities:
 Quantity   
 Description  
center9.value
the position of the center of masscenter10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=170,171
The CENTER action with label center10 calculates the following quantities:
 Quantity   
 Description  
center10.value
the position of the center of masscenter11: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=188,189
The CENTER action with label center11 calculates the following quantities:
 Quantity   
 Description  
center11.value
the position of the center of masscenter12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=206,207
The CENTER action with label center12 calculates the following quantities:
 Quantity   
 Description  
center12.value
the position of the center of masscenter13: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=224,225
The CENTER action with label center13 calculates the following quantities:
 Quantity   
 Description  
center13.value
the position of the center of masscenter14: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=242,243
The CENTER action with label center14 calculates the following quantities:
 Quantity   
 Description  
center14.value
the position of the center of masscenter15: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=260,261
The CENTER action with label center15 calculates the following quantities:
 Quantity   
 Description  
center15.value
the position of the center of masscenter16: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=278,279
The CENTER action with label center16 calculates the following quantities:
 Quantity   
 Description  
center16.value
the position of the center of masscenter17: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=296,297
The CENTER action with label center17 calculates the following quantities:
 Quantity   
 Description  
center17.value
the position of the center of masscenter18: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=314,315
The CENTER action with label center18 calculates the following quantities:
 Quantity   
 Description  
center18.value
the position of the center of masscenter19: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=332,333
The CENTER action with label center19 calculates the following quantities:
 Quantity   
 Description  
center19.value
the position of the center of masscenter20: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=350,351
The CENTER action with label center20 calculates the following quantities:
 Quantity   
 Description  
center20.value
the position of the center of masscenter21: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=368,369
The CENTER action with label center21 calculates the following quantities:
 Quantity   
 Description  
center21.value
the position of the center of masscenter22: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=386,387
The CENTER action with label center22 calculates the following quantities:
 Quantity   
 Description  
center22.value
the position of the center of masscenter23: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=404,405
The CENTER action with label center23 calculates the following quantities:
 Quantity   
 Description  
center23.value
the position of the center of masscenter24: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=422,423
The CENTER action with label center24 calculates the following quantities:
 Quantity   
 Description  
center24.value
the position of the center of masscenter25: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=440,441
The CENTER action with label center25 calculates the following quantities:
 Quantity   
 Description  
center25.value
the position of the center of masscenter26: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=458,459
The CENTER action with label center26 calculates the following quantities:
 Quantity   
 Description  
center26.value
the position of the center of masscenter27: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=476,477
The CENTER action with label center27 calculates the following quantities:
 Quantity   
 Description  
center27.value
the position of the center of masscenter28: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=494,495
The CENTER action with label center28 calculates the following quantities:
 Quantity   
 Description  
center28.value
the position of the center of masscenter29: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=512,513
The CENTER action with label center29 calculates the following quantities:
 Quantity   
 Description  
center29.value
the position of the center of masscenter30: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=530,531
The CENTER action with label center30 calculates the following quantities:
 Quantity   
 Description  
center30.value
the position of the center of masscenter31: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=548,549
The CENTER action with label center31 calculates the following quantities:
 Quantity   
 Description  
center31.value
the position of the center of masscenter32: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=566,567
The CENTER action with label center32 calculates the following quantities:
 Quantity   
 Description  
center32.value
the position of the center of masscenter33: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=584,585
The CENTER action with label center33 calculates the following quantities:
 Quantity   
 Description  
center33.value
the position of the center of masscenter34: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=602,603
The CENTER action with label center34 calculates the following quantities:
 Quantity   
 Description  
center34.value
the position of the center of masscenter35: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=620,621
The CENTER action with label center35 calculates the following quantities:
 Quantity   
 Description  
center35.value
the position of the center of masscenter36: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=638,639
The CENTER action with label center36 calculates the following quantities:
 Quantity   
 Description  
center36.value
the position of the center of massCENTERS: 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=center1,center2,center3,center4,center5,center6,center7,center8,center9,center10,center11,center12,center13,center14,center15,center16,center17,center18,center19,center20,center21,center22,center23,center24,center25,center26,center27,center28,center29,center30,center31,center32,center33,center34,center35,center36
# --- End of included input --- 
# Define the CV

The GROUP action with label CENTERS calculates somethingPAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=s1
 CENTER=CENTERS
 START=STARTS
 END=ENDS
 MAXR=0.7
 SIGMA=0.05,0.125
 #REFERENCE_DENSITY=4.5
 UP_DOWN_SYMMETRY
 LOW_COMM
... PAIR_ORIENTATIONAL_ENTROPY

PAIR_ORIENTATIONAL_ENTROPY_PERPENDICULARThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=s2
 CENTER=CENTERS
 START1=STARTS
 END1=ENDS
 START2=C8
 END2=C9
 MAXR=0.7
 SIGMA=0.05,0.125
 #REFERENCE_DENSITY=4.5
 UP_DOWN_SYMMETRY
 LOW_COMM
... PAIR_ORIENTATIONAL_ENTROPY_PERPENDICULAR

# Construct a bias potential using metadynamics

METADUsed to performed metadynamics on one or more collective variables. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=metad
 ARGthe labels of the scalars on which the bias will act=s1,s2   # Label of the CV
 PACEthe frequency for hill addition=500   # Pace in the deposition of the gaussians
 HEIGHTthe heights of the Gaussian hills=12.25   # Height of the gaussians in energy units kJ/mol. This is 2 kT.
 SIGMAthe widths of the Gaussian hills=0.2,0.2    # Width of the gaussian in CV units
 FILE a file in which the list of added hills is stored=HILLS   # File where the information of the gaussians is printed
 BIASFACTORuse well tempered metadynamics and use this bias factor=200.0   # Bias factor in well tempered simulations
 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0   # Temperature in Kelvin. Only needed for well tempered simulations
 GRID_MINthe lower bounds for the grid=-20.0,-20.0   # The following three lines define a grid for the calculation of the bias potential. Use it **always**.
 GRID_MAXthe upper bounds for the grid=0.,0.
 GRID_BINthe number of bins for the grid=1000,1000
 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD

# Restraint the volume
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor c(t)vol: VOLUMECalculate the volume the simulation box. More details

The VOLUME action with label vol calculates the volume of simulation boxUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=vol ATthe positions of the wall=12.0 KAPPAthe force constant for the wall=1000.0 EXP the powers for the walls=1 LABELa label for the action so that its output can be referenced in the input to other actions=uwall

# Print value of the CV and bias to a file named COLVAR
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 potentialPRINTPrint 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