Project ID: plumID:21.046
Source: WT-metaD.c22star/plumed2.dat
Originally used with PLUMED version: 2.3
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes
tested onv2.9
tested onmaster
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
ENTITY0
the atoms that make up a molecule that you wish to align
=5,12,24,43,54,61,78,89,100,119,131,142,157,183,195,205,219,230,241,248,258,277,284,295,307,326,333,345,355,372,383,398,413,425,442,461,478,488,498,514,528,545,556,575,590,604,620,644,658,670,689,711,725,740,747,769
all:
GROUP
Define 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
ATOMS
the numerical indexes for the set of atoms in the group
=5,12,24,43,54,61,78,89,100,119,131,142,157,183,195,205,219,230,241,248,258,277,284,295,307,326,333,345,355,372,383,398,413,425,442,461,478,488,498,514,528,545,556,575,590,604,620,644,658,670,689,711,725,740,747,769
rg:
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=all
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=rg
AT
the positions of the wall
=3.5
KAPPA
the force constant for the wall
=1000.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=rg
AT
the positions of the wall
=0.8
KAPPA
the force constant for the wall
=1000.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall
ALPHABETA
Calculate the alpha beta CV More details
...
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=1,5,8,10
REFERENCE
the reference values for each of the torsional angles
=-0.78540
ATOMS2
the atoms involved for each of the torsions you wish to calculate
=10,12,20,22
ATOMS3
the atoms involved for each of the torsions you wish to calculate
=22,24,39,41
ATOMS4
the atoms involved for each of the torsions you wish to calculate
=41,43,50,52
ATOMS5
the atoms involved for each of the torsions you wish to calculate
=52,54,57,59
ATOMS6
the atoms involved for each of the torsions you wish to calculate
=59,61,74,76
ATOMS7
the atoms involved for each of the torsions you wish to calculate
=76,78,85,87
ATOMS8
the atoms involved for each of the torsions you wish to calculate
=87,89,96,98
ATOMS9
the atoms involved for each of the torsions you wish to calculate
=98,100,113,115
ATOMS10
the atoms involved for each of the torsions you wish to calculate
=115,119,127,129
ATOMS11
the atoms involved for each of the torsions you wish to calculate
=129,131,138,140
ATOMS12
the atoms involved for each of the torsions you wish to calculate
=140,142,153,155
ATOMS13
the atoms involved for each of the torsions you wish to calculate
=155,157,177,179
ATOMS14
the atoms involved for each of the torsions you wish to calculate
=179,183,191,193
ATOMS15
the atoms involved for each of the torsions you wish to calculate
=193,195,201,203
ATOMS16
the atoms involved for each of the torsions you wish to calculate
=203,205,215,217
ATOMS17
the atoms involved for each of the torsions you wish to calculate
=217,219,226,228
ATOMS18
the atoms involved for each of the torsions you wish to calculate
=228,230,237,239
ATOMS19
the atoms involved for each of the torsions you wish to calculate
=239,241,244,246
ATOMS20
the atoms involved for each of the torsions you wish to calculate
=246,248,254,256
ATOMS21
the atoms involved for each of the torsions you wish to calculate
=256,258,273,275
ATOMS22
the atoms involved for each of the torsions you wish to calculate
=275,277,280,282
ATOMS23
the atoms involved for each of the torsions you wish to calculate
=282,284,291,293
ATOMS24
the atoms involved for each of the torsions you wish to calculate
=293,295,303,305
ATOMS25
the atoms involved for each of the torsions you wish to calculate
=305,307,322,324
ATOMS26
the atoms involved for each of the torsions you wish to calculate
=324,326,329,331
ATOMS27
the atoms involved for each of the torsions you wish to calculate
=331,333,341,343
ATOMS28
the atoms involved for each of the torsions you wish to calculate
=343,345,351,353
ATOMS29
the atoms involved for each of the torsions you wish to calculate
=353,355,368,370
ATOMS30
the atoms involved for each of the torsions you wish to calculate
=370,372,379,381
ATOMS31
the atoms involved for each of the torsions you wish to calculate
=381,383,394,396
ATOMS32
the atoms involved for each of the torsions you wish to calculate
=396,398,409,411
ATOMS33
the atoms involved for each of the torsions you wish to calculate
=411,413,421,423
ATOMS34
the atoms involved for each of the torsions you wish to calculate
=423,425,438,440
ATOMS35
the atoms involved for each of the torsions you wish to calculate
=440,442,457,459
ATOMS36
the atoms involved for each of the torsions you wish to calculate
=459,461,474,476
ATOMS37
the atoms involved for each of the torsions you wish to calculate
=476,478,484,486
ATOMS38
the atoms involved for each of the torsions you wish to calculate
=486,488,494,496
ATOMS39
the atoms involved for each of the torsions you wish to calculate
=496,498,510,512
ATOMS40
the atoms involved for each of the torsions you wish to calculate
=512,514,524,526
ATOMS41
the atoms involved for each of the torsions you wish to calculate
=526,528,541,543
ATOMS42
the atoms involved for each of the torsions you wish to calculate
=543,545,552,554
ATOMS43
the atoms involved for each of the torsions you wish to calculate
=554,556,571,573
ATOMS44
the atoms involved for each of the torsions you wish to calculate
=573,575,586,588
ATOMS45
the atoms involved for each of the torsions you wish to calculate
=588,590,600,602
ATOMS46
the atoms involved for each of the torsions you wish to calculate
=602,604,616,618
ATOMS47
the atoms involved for each of the torsions you wish to calculate
=618,620,640,642
ATOMS48
the atoms involved for each of the torsions you wish to calculate
=642,644,654,656
ATOMS49
the atoms involved for each of the torsions you wish to calculate
=656,658,666,668
ATOMS50
the atoms involved for each of the torsions you wish to calculate
=668,670,685,687
ATOMS51
the atoms involved for each of the torsions you wish to calculate
=687,689,707,709
ATOMS52
the atoms involved for each of the torsions you wish to calculate
=709,711,721,723
ATOMS53
the atoms involved for each of the torsions you wish to calculate
=723,725,736,738
ATOMS54
the atoms involved for each of the torsions you wish to calculate
=738,740,743,745
ATOMS55
the atoms involved for each of the torsions you wish to calculate
=745,747,765,767
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ab ... ALPHABETA
METAD
Used to performed metadynamics on one or more collective variables. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=meta
ARG
the input for this action is the scalar output from one or more other actions
=rg,ab
SIGMA
the widths of the Gaussian hills
=0.2,1.0
HEIGHT
the heights of the Gaussian hills
=0.5
PACE
the frequency for hill addition
=1000
BIASFACTOR
use well tempered metadynamics and use this bias factor
=4
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298 ... METAD
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=rg,ab,meta.bias
STRIDE
the frequency with which the quantities of interest should be output
=1000
FILE
the name of the file on which to output these quantities
=COLVAR
ENDPLUMED
Terminate plumed input. More details
# original input file with plumed 1 syntax follows HILLS HEIGHT 0.5 W_STRIDE 1000 RESTART WELLTEMPERED SIMTEMP 298 BIASFACTOR 4 #PTMETAD PRINT W_STRIDE 1000 ALIGN_ATOMS LIST #CV1 Rg CA RGYR LIST SIGMA 0.2 #CV4 ALPHABETA NDIH 55 SIGMA 1.0 1 5 8 10 -0.78540 10 12 20 22 -0.78540 22 24 39 41 -0.78540 41 43 50 52 -0.78540 52 54 57 59 -0.78540 59 61 74 76 -0.78540 76 78 85 87 -0.78540 87 89 96 98 -0.78540 98 100 113 115 -0.78540 115 119 127 129 -0.78540 129 131 138 140 -0.78540 140 142 153 155 -0.78540 155 157 177 179 -0.78540 179 183 191 193 -0.78540 193 195 201 203 -0.78540 203 205 215 217 -0.78540 217 219 226 228 -0.78540 228 230 237 239 -0.78540 239 241 244 246 -0.78540 246 248 254 256 -0.78540 256 258 273 275 -0.78540 275 277 280 282 -0.78540 282 284 291 293 -0.78540 293 295 303 305 -0.78540 305 307 322 324 -0.78540 324 326 329 331 -0.78540 331 333 341 343 -0.78540 343 345 351 353 -0.78540 353 355 368 370 -0.78540 370 372 379 381 -0.78540 381 383 394 396 -0.78540 396 398 409 411 -0.78540 411 413 421 423 -0.78540 423 425 438 440 -0.78540 440 442 457 459 -0.78540 459 461 474 476 -0.78540 476 478 484 486 -0.78540 486 488 494 496 -0.78540 496 498 510 512 -0.78540 512 514 524 526 -0.78540 526 528 541 543 -0.78540 543 545 552 554 -0.78540 554 556 571 573 -0.78540 573 575 586 588 -0.78540 588 590 600 602 -0.78540 602 604 616 618 -0.78540 618 620 640 642 -0.78540 642 644 654 656 -0.78540 656 658 666 668 -0.78540 668 670 685 687 -0.78540 687 689 707 709 -0.78540 709 711 721 723 -0.78540 723 725 736 738 -0.78540 738 740 743 745 -0.78540 745 747 765 767 -0.78540 #UWALL CV 1 LIMIT 2.2 KAPPA 1000.0 #UWALL CV 2 LIMIT 0.6 KAPPA 1000.0 LWALL CV 1 LIMIT 0.8 KAPPA 1000.0 UWALL CV 1 LIMIT 3.5 KAPPA 1000.0 all-> 5 12 24 43 54 61 78 89 100 119 131 142 157 183 195 205 219 230 241 248 258 277 284 295 307 326 333 345 355 372 383 398 413 425 442 461 478 488 498 514 528 545 556 575 590 604 620 644 658 670 689 711 725 740 747 769 all<- ENDMETA </span></pre>