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
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
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
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
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
# INCLUDE FILE=centers.dat
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 appear in the definition of this center=1,2
The CENTER action with label start1 calculates the following quantities: Quantity | Description |
start1.value | the position of the center of mass |
start2: 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=19,20
The CENTER action with label start2 calculates the following quantities: Quantity | Description |
start2.value | the position of the center of mass |
start3: 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=37,38
The CENTER action with label start3 calculates the following quantities: Quantity | Description |
start3.value | the position of the center of mass |
start4: 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=55,56
The CENTER action with label start4 calculates the following quantities: Quantity | Description |
start4.value | the position of the center of mass |
start5: 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=73,74
The CENTER action with label start5 calculates the following quantities: Quantity | Description |
start5.value | the position of the center of mass |
start6: 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=91,92
The CENTER action with label start6 calculates the following quantities: Quantity | Description |
start6.value | the position of the center of mass |
start7: 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=109,110
The CENTER action with label start7 calculates the following quantities: Quantity | Description |
start7.value | the position of the center of mass |
start8: 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=127,128
The CENTER action with label start8 calculates the following quantities: Quantity | Description |
start8.value | the position of the center of mass |
start9: 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=145,146
The CENTER action with label start9 calculates the following quantities: Quantity | Description |
start9.value | the position of the center of mass |
start10: 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=163,164
The CENTER action with label start10 calculates the following quantities: Quantity | Description |
start10.value | the position of the center of mass |
start11: 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=181,182
The CENTER action with label start11 calculates the following quantities: Quantity | Description |
start11.value | the position of the center of mass |
start12: 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=199,200
The CENTER action with label start12 calculates the following quantities: Quantity | Description |
start12.value | the position of the center of mass |
start13: 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=217,218
The CENTER action with label start13 calculates the following quantities: Quantity | Description |
start13.value | the position of the center of mass |
start14: 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=235,236
The CENTER action with label start14 calculates the following quantities: Quantity | Description |
start14.value | the position of the center of mass |
start15: 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=253,254
The CENTER action with label start15 calculates the following quantities: Quantity | Description |
start15.value | the position of the center of mass |
start16: 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=271,272
The CENTER action with label start16 calculates the following quantities: Quantity | Description |
start16.value | the position of the center of mass |
start17: 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=289,290
The CENTER action with label start17 calculates the following quantities: Quantity | Description |
start17.value | the position of the center of mass |
start18: 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=307,308
The CENTER action with label start18 calculates the following quantities: Quantity | Description |
start18.value | the position of the center of mass |
start19: 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=325,326
The CENTER action with label start19 calculates the following quantities: Quantity | Description |
start19.value | the position of the center of mass |
start20: 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=343,344
The CENTER action with label start20 calculates the following quantities: Quantity | Description |
start20.value | the position of the center of mass |
start21: 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=361,362
The CENTER action with label start21 calculates the following quantities: Quantity | Description |
start21.value | the position of the center of mass |
start22: 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=379,380
The CENTER action with label start22 calculates the following quantities: Quantity | Description |
start22.value | the position of the center of mass |
start23: 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=397,398
The CENTER action with label start23 calculates the following quantities: Quantity | Description |
start23.value | the position of the center of mass |
start24: 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=415,416
The CENTER action with label start24 calculates the following quantities: Quantity | Description |
start24.value | the position of the center of mass |
start25: 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=433,434
The CENTER action with label start25 calculates the following quantities: Quantity | Description |
start25.value | the position of the center of mass |
start26: 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=451,452
The CENTER action with label start26 calculates the following quantities: Quantity | Description |
start26.value | the position of the center of mass |
start27: 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=469,470
The CENTER action with label start27 calculates the following quantities: Quantity | Description |
start27.value | the position of the center of mass |
start28: 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=487,488
The CENTER action with label start28 calculates the following quantities: Quantity | Description |
start28.value | the position of the center of mass |
start29: 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=505,506
The CENTER action with label start29 calculates the following quantities: Quantity | Description |
start29.value | the position of the center of mass |
start30: 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=523,524
The CENTER action with label start30 calculates the following quantities: Quantity | Description |
start30.value | the position of the center of mass |
start31: 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=541,542
The CENTER action with label start31 calculates the following quantities: Quantity | Description |
start31.value | the position of the center of mass |
start32: 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=559,560
The CENTER action with label start32 calculates the following quantities: Quantity | Description |
start32.value | the position of the center of mass |
start33: 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=577,578
The CENTER action with label start33 calculates the following quantities: Quantity | Description |
start33.value | the position of the center of mass |
start34: 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=595,596
The CENTER action with label start34 calculates the following quantities: Quantity | Description |
start34.value | the position of the center of mass |
start35: 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=613,614
The CENTER action with label start35 calculates the following quantities: Quantity | Description |
start35.value | the position of the center of mass |
start36: 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=631,632
The CENTER action with label start36 calculates the following quantities: Quantity | Description |
start36.value | the position of the center of mass |
STARTS: 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 appear in the definition of this center=5,7
The CENTER action with label end1 calculates the following quantities: Quantity | Description |
end1.value | the position of the center of mass |
end2: 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=23,25
The CENTER action with label end2 calculates the following quantities: Quantity | Description |
end2.value | the position of the center of mass |
end3: 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=41,43
The CENTER action with label end3 calculates the following quantities: Quantity | Description |
end3.value | the position of the center of mass |
end4: 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=59,61
The CENTER action with label end4 calculates the following quantities: Quantity | Description |
end4.value | the position of the center of mass |
end5: 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=77,79
The CENTER action with label end5 calculates the following quantities: Quantity | Description |
end5.value | the position of the center of mass |
end6: 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=95,97
The CENTER action with label end6 calculates the following quantities: Quantity | Description |
end6.value | the position of the center of mass |
end7: 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=113,115
The CENTER action with label end7 calculates the following quantities: Quantity | Description |
end7.value | the position of the center of mass |
end8: 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=131,133
The CENTER action with label end8 calculates the following quantities: Quantity | Description |
end8.value | the position of the center of mass |
end9: 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=149,151
The CENTER action with label end9 calculates the following quantities: Quantity | Description |
end9.value | the position of the center of mass |
end10: 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=167,169
The CENTER action with label end10 calculates the following quantities: Quantity | Description |
end10.value | the position of the center of mass |
end11: 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=185,187
The CENTER action with label end11 calculates the following quantities: Quantity | Description |
end11.value | the position of the center of mass |
end12: 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=203,205
The CENTER action with label end12 calculates the following quantities: Quantity | Description |
end12.value | the position of the center of mass |
end13: 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=221,223
The CENTER action with label end13 calculates the following quantities: Quantity | Description |
end13.value | the position of the center of mass |
end14: 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=239,241
The CENTER action with label end14 calculates the following quantities: Quantity | Description |
end14.value | the position of the center of mass |
end15: 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=257,259
The CENTER action with label end15 calculates the following quantities: Quantity | Description |
end15.value | the position of the center of mass |
end16: 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=275,277
The CENTER action with label end16 calculates the following quantities: Quantity | Description |
end16.value | the position of the center of mass |
end17: 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=293,295
The CENTER action with label end17 calculates the following quantities: Quantity | Description |
end17.value | the position of the center of mass |
end18: 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=311,313
The CENTER action with label end18 calculates the following quantities: Quantity | Description |
end18.value | the position of the center of mass |
end19: 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=329,331
The CENTER action with label end19 calculates the following quantities: Quantity | Description |
end19.value | the position of the center of mass |
end20: 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=347,349
The CENTER action with label end20 calculates the following quantities: Quantity | Description |
end20.value | the position of the center of mass |
end21: 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=365,367
The CENTER action with label end21 calculates the following quantities: Quantity | Description |
end21.value | the position of the center of mass |
end22: 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=383,385
The CENTER action with label end22 calculates the following quantities: Quantity | Description |
end22.value | the position of the center of mass |
end23: 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=401,403
The CENTER action with label end23 calculates the following quantities: Quantity | Description |
end23.value | the position of the center of mass |
end24: 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=419,421
The CENTER action with label end24 calculates the following quantities: Quantity | Description |
end24.value | the position of the center of mass |
end25: 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=437,439
The CENTER action with label end25 calculates the following quantities: Quantity | Description |
end25.value | the position of the center of mass |
end26: 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=455,457
The CENTER action with label end26 calculates the following quantities: Quantity | Description |
end26.value | the position of the center of mass |
end27: 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=473,475
The CENTER action with label end27 calculates the following quantities: Quantity | Description |
end27.value | the position of the center of mass |
end28: 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=491,493
The CENTER action with label end28 calculates the following quantities: Quantity | Description |
end28.value | the position of the center of mass |
end29: 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=509,511
The CENTER action with label end29 calculates the following quantities: Quantity | Description |
end29.value | the position of the center of mass |
end30: 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=527,529
The CENTER action with label end30 calculates the following quantities: Quantity | Description |
end30.value | the position of the center of mass |
end31: 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=545,547
The CENTER action with label end31 calculates the following quantities: Quantity | Description |
end31.value | the position of the center of mass |
end32: 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=563,565
The CENTER action with label end32 calculates the following quantities: Quantity | Description |
end32.value | the position of the center of mass |
end33: 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=581,583
The CENTER action with label end33 calculates the following quantities: Quantity | Description |
end33.value | the position of the center of mass |
end34: 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=599,601
The CENTER action with label end34 calculates the following quantities: Quantity | Description |
end34.value | the position of the center of mass |
end35: 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=617,619
The CENTER action with label end35 calculates the following quantities: Quantity | Description |
end35.value | the position of the center of mass |
end36: 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=635,637
The CENTER action with label end36 calculates the following quantities: Quantity | Description |
end36.value | the position of the center of mass |
ENDS: 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 appear in the definition of this center=8,9
The CENTER action with label center1 calculates the following quantities: Quantity | Description |
center1.value | the position of the center of mass |
center2: 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=26,27
The CENTER action with label center2 calculates the following quantities: Quantity | Description |
center2.value | the position of the center of mass |
center3: 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=44,45
The CENTER action with label center3 calculates the following quantities: Quantity | Description |
center3.value | the position of the center of mass |
center4: 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=62,63
The CENTER action with label center4 calculates the following quantities: Quantity | Description |
center4.value | the position of the center of mass |
center5: 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=80,81
The CENTER action with label center5 calculates the following quantities: Quantity | Description |
center5.value | the position of the center of mass |
center6: 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=98,99
The CENTER action with label center6 calculates the following quantities: Quantity | Description |
center6.value | the position of the center of mass |
center7: 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=116,117
The CENTER action with label center7 calculates the following quantities: Quantity | Description |
center7.value | the position of the center of mass |
center8: 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=134,135
The CENTER action with label center8 calculates the following quantities: Quantity | Description |
center8.value | the position of the center of mass |
center9: 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=152,153
The CENTER action with label center9 calculates the following quantities: Quantity | Description |
center9.value | the position of the center of mass |
center10: 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=170,171
The CENTER action with label center10 calculates the following quantities: Quantity | Description |
center10.value | the position of the center of mass |
center11: 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=188,189
The CENTER action with label center11 calculates the following quantities: Quantity | Description |
center11.value | the position of the center of mass |
center12: 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=206,207
The CENTER action with label center12 calculates the following quantities: Quantity | Description |
center12.value | the position of the center of mass |
center13: 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=224,225
The CENTER action with label center13 calculates the following quantities: Quantity | Description |
center13.value | the position of the center of mass |
center14: 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=242,243
The CENTER action with label center14 calculates the following quantities: Quantity | Description |
center14.value | the position of the center of mass |
center15: 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=260,261
The CENTER action with label center15 calculates the following quantities: Quantity | Description |
center15.value | the position of the center of mass |
center16: 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=278,279
The CENTER action with label center16 calculates the following quantities: Quantity | Description |
center16.value | the position of the center of mass |
center17: 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=296,297
The CENTER action with label center17 calculates the following quantities: Quantity | Description |
center17.value | the position of the center of mass |
center18: 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=314,315
The CENTER action with label center18 calculates the following quantities: Quantity | Description |
center18.value | the position of the center of mass |
center19: 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=332,333
The CENTER action with label center19 calculates the following quantities: Quantity | Description |
center19.value | the position of the center of mass |
center20: 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=350,351
The CENTER action with label center20 calculates the following quantities: Quantity | Description |
center20.value | the position of the center of mass |
center21: 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=368,369
The CENTER action with label center21 calculates the following quantities: Quantity | Description |
center21.value | the position of the center of mass |
center22: 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=386,387
The CENTER action with label center22 calculates the following quantities: Quantity | Description |
center22.value | the position of the center of mass |
center23: 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=404,405
The CENTER action with label center23 calculates the following quantities: Quantity | Description |
center23.value | the position of the center of mass |
center24: 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=422,423
The CENTER action with label center24 calculates the following quantities: Quantity | Description |
center24.value | the position of the center of mass |
center25: 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=440,441
The CENTER action with label center25 calculates the following quantities: Quantity | Description |
center25.value | the position of the center of mass |
center26: 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=458,459
The CENTER action with label center26 calculates the following quantities: Quantity | Description |
center26.value | the position of the center of mass |
center27: 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=476,477
The CENTER action with label center27 calculates the following quantities: Quantity | Description |
center27.value | the position of the center of mass |
center28: 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=494,495
The CENTER action with label center28 calculates the following quantities: Quantity | Description |
center28.value | the position of the center of mass |
center29: 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=512,513
The CENTER action with label center29 calculates the following quantities: Quantity | Description |
center29.value | the position of the center of mass |
center30: 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=530,531
The CENTER action with label center30 calculates the following quantities: Quantity | Description |
center30.value | the position of the center of mass |
center31: 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=548,549
The CENTER action with label center31 calculates the following quantities: Quantity | Description |
center31.value | the position of the center of mass |
center32: 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=566,567
The CENTER action with label center32 calculates the following quantities: Quantity | Description |
center32.value | the position of the center of mass |
center33: 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=584,585
The CENTER action with label center33 calculates the following quantities: Quantity | Description |
center33.value | the position of the center of mass |
center34: 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=602,603
The CENTER action with label center34 calculates the following quantities: Quantity | Description |
center34.value | the position of the center of mass |
center35: 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=620,621
The CENTER action with label center35 calculates the following quantities: Quantity | Description |
center35.value | the position of the center of mass |
center36: 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=638,639
The CENTER action with label center36 calculates the following quantities: Quantity | Description |
center36.value | the position of the center of mass |
CENTERS: 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 ---
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
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
UP_DOWN_SYMMETRY
LOW_COMM
... PAIR_ORIENTATIONAL_ENTROPY_PERPENDICULAR
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
PACEthe frequency for hill addition=500
HEIGHTthe heights of the Gaussian hills=12.25
SIGMAthe widths of the Gaussian hills=0.2,0.2
FILE a file in which the list of added hills is stored=HILLS
BIASFACTORuse well tempered metadynamics and use this bias factor=200.0
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
GRID_MINthe lower bounds for the grid=-20.0,-20.0
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
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
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 potential |
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR