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 onv2.10
tested onmaster
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the 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:  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=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:   GYRATIONCalculate the radius of gyration, or other properties related to it. More details  ATOMSthe group of atoms that you are calculating the Gyration Tensor for=all
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rg ATthe positions of the wall=3.5 KAPPAthe force constant for the wall=1000.0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rg ATthe positions of the wall=0.8 KAPPAthe force constant for the wall=1000.0 LABELa label for the action so that its output can be referenced in the input to other actions=lwall

ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ... ATOMS1the atoms involved for each of the torsions you wish to calculate=1,5,8,10 REFERENCEthe reference values for each of the torsional angles=-0.78540 ATOMS2the atoms involved for each of the torsions you wish to calculate=10,12,20,22 ATOMS3the atoms involved for each of the torsions you wish to calculate=22,24,39,41 ATOMS4the atoms involved for each of the torsions you wish to calculate=41,43,50,52 ATOMS5the atoms involved for each of the torsions you wish to calculate=52,54,57,59 ATOMS6the atoms involved for each of the torsions you wish to calculate=59,61,74,76 ATOMS7the atoms involved for each of the torsions you wish to calculate=76,78,85,87 ATOMS8the atoms involved for each of the torsions you wish to calculate=87,89,96,98 ATOMS9the atoms involved for each of the torsions you wish to calculate=98,100,113,115 ATOMS10the atoms involved for each of the torsions you wish to calculate=115,119,127,129 ATOMS11the atoms involved for each of the torsions you wish to calculate=129,131,138,140 ATOMS12the atoms involved for each of the torsions you wish to calculate=140,142,153,155 ATOMS13the atoms involved for each of the torsions you wish to calculate=155,157,177,179 ATOMS14the atoms involved for each of the torsions you wish to calculate=179,183,191,193 ATOMS15the atoms involved for each of the torsions you wish to calculate=193,195,201,203 ATOMS16the atoms involved for each of the torsions you wish to calculate=203,205,215,217 ATOMS17the atoms involved for each of the torsions you wish to calculate=217,219,226,228 ATOMS18the atoms involved for each of the torsions you wish to calculate=228,230,237,239 ATOMS19the atoms involved for each of the torsions you wish to calculate=239,241,244,246 ATOMS20the atoms involved for each of the torsions you wish to calculate=246,248,254,256 ATOMS21the atoms involved for each of the torsions you wish to calculate=256,258,273,275 ATOMS22the atoms involved for each of the torsions you wish to calculate=275,277,280,282 ATOMS23the atoms involved for each of the torsions you wish to calculate=282,284,291,293 ATOMS24the atoms involved for each of the torsions you wish to calculate=293,295,303,305 ATOMS25the atoms involved for each of the torsions you wish to calculate=305,307,322,324 ATOMS26the atoms involved for each of the torsions you wish to calculate=324,326,329,331 ATOMS27the atoms involved for each of the torsions you wish to calculate=331,333,341,343 ATOMS28the atoms involved for each of the torsions you wish to calculate=343,345,351,353 ATOMS29the atoms involved for each of the torsions you wish to calculate=353,355,368,370 ATOMS30the atoms involved for each of the torsions you wish to calculate=370,372,379,381 ATOMS31the atoms involved for each of the torsions you wish to calculate=381,383,394,396 ATOMS32the atoms involved for each of the torsions you wish to calculate=396,398,409,411 ATOMS33the atoms involved for each of the torsions you wish to calculate=411,413,421,423 ATOMS34the atoms involved for each of the torsions you wish to calculate=423,425,438,440 ATOMS35the atoms involved for each of the torsions you wish to calculate=440,442,457,459 ATOMS36the atoms involved for each of the torsions you wish to calculate=459,461,474,476 ATOMS37the atoms involved for each of the torsions you wish to calculate=476,478,484,486 ATOMS38the atoms involved for each of the torsions you wish to calculate=486,488,494,496 ATOMS39the atoms involved for each of the torsions you wish to calculate=496,498,510,512 ATOMS40the atoms involved for each of the torsions you wish to calculate=512,514,524,526 ATOMS41the atoms involved for each of the torsions you wish to calculate=526,528,541,543 ATOMS42the atoms involved for each of the torsions you wish to calculate=543,545,552,554 ATOMS43the atoms involved for each of the torsions you wish to calculate=554,556,571,573 ATOMS44the atoms involved for each of the torsions you wish to calculate=573,575,586,588 ATOMS45the atoms involved for each of the torsions you wish to calculate=588,590,600,602 ATOMS46the atoms involved for each of the torsions you wish to calculate=602,604,616,618 ATOMS47the atoms involved for each of the torsions you wish to calculate=618,620,640,642 ATOMS48the atoms involved for each of the torsions you wish to calculate=642,644,654,656 ATOMS49the atoms involved for each of the torsions you wish to calculate=656,658,666,668 ATOMS50the atoms involved for each of the torsions you wish to calculate=668,670,685,687 ATOMS51the atoms involved for each of the torsions you wish to calculate=687,689,707,709 ATOMS52the atoms involved for each of the torsions you wish to calculate=709,711,721,723 ATOMS53the atoms involved for each of the torsions you wish to calculate=723,725,736,738 ATOMS54the atoms involved for each of the torsions you wish to calculate=738,740,743,745 ATOMS55the atoms involved for each of the torsions you wish to calculate=745,747,765,767 LABELa label for the action so that its output can be referenced in the input to other actions=ab ... ALPHABETA
METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=meta ARGthe labels of the scalars on which the bias will act=rg,ab SIGMAthe widths of the Gaussian hills=0.2,1.0 HEIGHTthe heights of the Gaussian hills=0.5 PACEthe frequency for hill addition=1000 BIASFACTORuse well tempered metadynamics and use this bias factor=4 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298 ... METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rg,ab,meta.bias STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=COLVAR ENDPLUMEDTerminate 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 <all> #CV1 Rg CA RGYR LIST <all> 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