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
# Restart simulation. This command will append results of new simulations to the same output files, e.g. COLVAR. # RESTARTLOADLoads a library, possibly defining new actions. More detailsFILE=PairOrientationalEntropy.cpp The LOAD action with label calculates somethingfile to be loadedLOADLoads a library, possibly defining new actions. More detailsFILE=PairOrientationalEntropyPerpendicular.cppfile to be loaded
# 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 detailsATOMS=8-648:18 # Head The GROUP action with label C8 calculates somethingC9:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=9-648:18 # Head The GROUP action with label C9 calculates somethingthe numerical indexes for the set of atoms in the groupINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=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:file to be includedCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1,2 The CENTER action with label start1 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart2:
Quantity Description start1.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=19,20 The CENTER action with label start2 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart3:
Quantity Description start2.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=37,38 The CENTER action with label start3 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart4:
Quantity Description start3.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=55,56 The CENTER action with label start4 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart5:
Quantity Description start4.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=73,74 The CENTER action with label start5 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart6:
Quantity Description start5.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=91,92 The CENTER action with label start6 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart7:
Quantity Description start6.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=109,110 The CENTER action with label start7 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart8:
Quantity Description start7.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=127,128 The CENTER action with label start8 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart9:
Quantity Description start8.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=145,146 The CENTER action with label start9 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart10:
Quantity Description start9.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=163,164 The CENTER action with label start10 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart11:
Quantity Description start10.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=181,182 The CENTER action with label start11 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart12:
Quantity Description start11.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=199,200 The CENTER action with label start12 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart13:
Quantity Description start12.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=217,218 The CENTER action with label start13 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart14:
Quantity Description start13.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=235,236 The CENTER action with label start14 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart15:
Quantity Description start14.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=253,254 The CENTER action with label start15 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart16:
Quantity Description start15.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=271,272 The CENTER action with label start16 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart17:
Quantity Description start16.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=289,290 The CENTER action with label start17 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart18:
Quantity Description start17.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=307,308 The CENTER action with label start18 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart19:
Quantity Description start18.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=325,326 The CENTER action with label start19 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart20:
Quantity Description start19.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=343,344 The CENTER action with label start20 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart21:
Quantity Description start20.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=361,362 The CENTER action with label start21 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart22:
Quantity Description start21.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=379,380 The CENTER action with label start22 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart23:
Quantity Description start22.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=397,398 The CENTER action with label start23 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart24:
Quantity Description start23.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=415,416 The CENTER action with label start24 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart25:
Quantity Description start24.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=433,434 The CENTER action with label start25 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart26:
Quantity Description start25.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=451,452 The CENTER action with label start26 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart27:
Quantity Description start26.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=469,470 The CENTER action with label start27 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart28:
Quantity Description start27.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=487,488 The CENTER action with label start28 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart29:
Quantity Description start28.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=505,506 The CENTER action with label start29 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart30:
Quantity Description start29.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=523,524 The CENTER action with label start30 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart31:
Quantity Description start30.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=541,542 The CENTER action with label start31 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart32:
Quantity Description start31.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=559,560 The CENTER action with label start32 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart33:
Quantity Description start32.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=577,578 The CENTER action with label start33 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart34:
Quantity Description start33.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=595,596 The CENTER action with label start34 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart35:
Quantity Description start34.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=613,614 The CENTER action with label start35 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forstart36:
Quantity Description start35.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=631,632 The CENTER action with label start36 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forSTARTS:
Quantity Description start36.value the position of the center of mass 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 detailsATOMS=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:the numerical indexes for the set of atoms in the groupCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=5,7 The CENTER action with label end1 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend2:
Quantity Description end1.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=23,25 The CENTER action with label end2 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend3:
Quantity Description end2.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=41,43 The CENTER action with label end3 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend4:
Quantity Description end3.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=59,61 The CENTER action with label end4 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend5:
Quantity Description end4.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=77,79 The CENTER action with label end5 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend6:
Quantity Description end5.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=95,97 The CENTER action with label end6 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend7:
Quantity Description end6.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=113,115 The CENTER action with label end7 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend8:
Quantity Description end7.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=131,133 The CENTER action with label end8 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend9:
Quantity Description end8.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=149,151 The CENTER action with label end9 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend10:
Quantity Description end9.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=167,169 The CENTER action with label end10 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend11:
Quantity Description end10.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=185,187 The CENTER action with label end11 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend12:
Quantity Description end11.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=203,205 The CENTER action with label end12 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend13:
Quantity Description end12.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=221,223 The CENTER action with label end13 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend14:
Quantity Description end13.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=239,241 The CENTER action with label end14 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend15:
Quantity Description end14.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=257,259 The CENTER action with label end15 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend16:
Quantity Description end15.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=275,277 The CENTER action with label end16 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend17:
Quantity Description end16.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=293,295 The CENTER action with label end17 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend18:
Quantity Description end17.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=311,313 The CENTER action with label end18 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend19:
Quantity Description end18.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=329,331 The CENTER action with label end19 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend20:
Quantity Description end19.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=347,349 The CENTER action with label end20 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend21:
Quantity Description end20.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=365,367 The CENTER action with label end21 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend22:
Quantity Description end21.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=383,385 The CENTER action with label end22 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend23:
Quantity Description end22.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=401,403 The CENTER action with label end23 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend24:
Quantity Description end23.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=419,421 The CENTER action with label end24 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend25:
Quantity Description end24.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=437,439 The CENTER action with label end25 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend26:
Quantity Description end25.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=455,457 The CENTER action with label end26 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend27:
Quantity Description end26.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=473,475 The CENTER action with label end27 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend28:
Quantity Description end27.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=491,493 The CENTER action with label end28 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend29:
Quantity Description end28.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=509,511 The CENTER action with label end29 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend30:
Quantity Description end29.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=527,529 The CENTER action with label end30 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend31:
Quantity Description end30.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=545,547 The CENTER action with label end31 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend32:
Quantity Description end31.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=563,565 The CENTER action with label end32 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend33:
Quantity Description end32.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=581,583 The CENTER action with label end33 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend34:
Quantity Description end33.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=599,601 The CENTER action with label end34 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend35:
Quantity Description end34.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=617,619 The CENTER action with label end35 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forend36:
Quantity Description end35.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=635,637 The CENTER action with label end36 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forENDS:
Quantity Description end36.value the position of the center of mass 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 detailsATOMS=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:the numerical indexes for the set of atoms in the groupCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=8,9 The CENTER action with label center1 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter2:
Quantity Description center1.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=26,27 The CENTER action with label center2 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter3:
Quantity Description center2.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=44,45 The CENTER action with label center3 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter4:
Quantity Description center3.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=62,63 The CENTER action with label center4 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter5:
Quantity Description center4.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=80,81 The CENTER action with label center5 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter6:
Quantity Description center5.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=98,99 The CENTER action with label center6 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter7:
Quantity Description center6.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=116,117 The CENTER action with label center7 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter8:
Quantity Description center7.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=134,135 The CENTER action with label center8 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter9:
Quantity Description center8.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=152,153 The CENTER action with label center9 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter10:
Quantity Description center9.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=170,171 The CENTER action with label center10 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter11:
Quantity Description center10.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=188,189 The CENTER action with label center11 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter12:
Quantity Description center11.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=206,207 The CENTER action with label center12 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter13:
Quantity Description center12.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=224,225 The CENTER action with label center13 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter14:
Quantity Description center13.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=242,243 The CENTER action with label center14 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter15:
Quantity Description center14.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=260,261 The CENTER action with label center15 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter16:
Quantity Description center15.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=278,279 The CENTER action with label center16 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter17:
Quantity Description center16.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=296,297 The CENTER action with label center17 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter18:
Quantity Description center17.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=314,315 The CENTER action with label center18 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter19:
Quantity Description center18.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=332,333 The CENTER action with label center19 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter20:
Quantity Description center19.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=350,351 The CENTER action with label center20 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter21:
Quantity Description center20.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=368,369 The CENTER action with label center21 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter22:
Quantity Description center21.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=386,387 The CENTER action with label center22 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter23:
Quantity Description center22.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=404,405 The CENTER action with label center23 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter24:
Quantity Description center23.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=422,423 The CENTER action with label center24 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter25:
Quantity Description center24.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=440,441 The CENTER action with label center25 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter26:
Quantity Description center25.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=458,459 The CENTER action with label center26 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter27:
Quantity Description center26.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=476,477 The CENTER action with label center27 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter28:
Quantity Description center27.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=494,495 The CENTER action with label center28 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter29:
Quantity Description center28.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=512,513 The CENTER action with label center29 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter30:
Quantity Description center29.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=530,531 The CENTER action with label center30 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter31:
Quantity Description center30.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=548,549 The CENTER action with label center31 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter32:
Quantity Description center31.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=566,567 The CENTER action with label center32 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter33:
Quantity Description center32.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=584,585 The CENTER action with label center33 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter34:
Quantity Description center33.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=602,603 The CENTER action with label center34 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter35:
Quantity Description center34.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=620,621 The CENTER action with label center35 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forcenter36:
Quantity Description center35.value the position of the center of mass CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=638,639 The CENTER action with label center36 calculates the following quantities:the group of atoms that you are calculating the Gyration Tensor forCENTERS:
Quantity Description center36.value the position of the center of mass 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 detailsATOMS=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 numerical indexes for the set of atoms in the group
# Define the CV
The GROUP action with label CENTERS calculates somethingPAIR_ORIENTATIONAL_ENTROPY... 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_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More detailsPAIR_ORIENTATIONAL_ENTROPY_PERPENDICULAR... 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_PERPENDICULARThis action is not part of PLUMED and was included by using a LOAD command More details
# Construct a bias potential using metadynamicsMETAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=metada label for the action so that its output can be referenced in the input to other actionsARG=s1,s2 # Label of the CVthe input for this action is the scalar output from one or more other actionsPACE=500 # Pace in the deposition of the gaussiansthe frequency for hill additionHEIGHT=12.25 # Height of the gaussians in energy units kJ/mol. This is 2 kT.the heights of the Gaussian hillsSIGMA=0.2,0.2 # Width of the gaussian in CV unitsthe widths of the Gaussian hillsFILE=HILLS # File where the information of the gaussians is printeda file in which the list of added hills is storedBIASFACTOR=200.0 # Bias factor in well tempered simulationsuse well tempered metadynamics and use this bias factorTEMP=300.0 # Temperature in Kelvin. Only needed for well tempered simulationsthe system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=-20.0,-20.0 # The following three lines define a grid for the calculation of the bias potential. Use it **always**.the lower bounds for the gridGRID_MAX=0.,0the upper bounds for the gridGRID_BIN=1000,1000the number of bins for the gridCALC_RCT... METADcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
# Restraint the volume The METAD action with label metad calculates the following quantities:vol:
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) VOLUMECalculate the volume of 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 detailsARG=volthe arguments on which the bias is actingAT=12.0the positions of the wallKAPPA=1000.0the force constant for the wallEXP=1the powers for the wallsLABEL=uwalla label for the action so that its output can be referenced in the input to other actions
# 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 potential Print quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantities