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
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=5,12,24,43,54,61,78,89,100,119,131,142,157,183,195,205,219,230,241,248,258,277,284,295,307,326,333,345,355,372,383,398,413,425,442,461,478,488,498,514,528,545,556,575,590,604,620,644,658,670,689,711,725,740,747,769the atoms that make up a molecule that you wish to align
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 detailsATOMS=5,12,24,43,54,61,78,89,100,119,131,142,157,183,195,205,219,230,241,248,258,277,284,295,307,326,333,345,355,372,383,398,413,425,442,461,478,488,498,514,528,545,556,575,590,604,620,644,658,670,689,711,725,740,747,769the numerical indexes for the set of atoms in the group
rg:GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsATOMS=allthe group of atoms that you are calculating the Gyration Tensor forUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rgthe arguments on which the bias is actingAT=3.5the positions of the wallKAPPA=1000.0the force constant for the wallLABEL=uwalla label for the action so that its output can be referenced in the input to other actionsLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rgthe arguments on which the bias is actingAT=0.8the positions of the wallKAPPA=1000.0the force constant for the wallLABEL=lwalla label for the action so that its output can be referenced in the input to other actionsALPHABETA...Calculate the alpha beta CV More detailsATOMS1=1,5,8,10the atoms involved for each of the torsions you wish to calculateREFERENCE=-0.78540the reference values for each of the torsional anglesATOMS2=10,12,20,22the atoms involved for each of the torsions you wish to calculateATOMS3=22,24,39,41the atoms involved for each of the torsions you wish to calculateATOMS4=41,43,50,52the atoms involved for each of the torsions you wish to calculateATOMS5=52,54,57,59the atoms involved for each of the torsions you wish to calculateATOMS6=59,61,74,76the atoms involved for each of the torsions you wish to calculateATOMS7=76,78,85,87the atoms involved for each of the torsions you wish to calculateATOMS8=87,89,96,98the atoms involved for each of the torsions you wish to calculateATOMS9=98,100,113,115the atoms involved for each of the torsions you wish to calculateATOMS10=115,119,127,129the atoms involved for each of the torsions you wish to calculateATOMS11=129,131,138,140the atoms involved for each of the torsions you wish to calculateATOMS12=140,142,153,155the atoms involved for each of the torsions you wish to calculateATOMS13=155,157,177,179the atoms involved for each of the torsions you wish to calculateATOMS14=179,183,191,193the atoms involved for each of the torsions you wish to calculateATOMS15=193,195,201,203the atoms involved for each of the torsions you wish to calculateATOMS16=203,205,215,217the atoms involved for each of the torsions you wish to calculateATOMS17=217,219,226,228the atoms involved for each of the torsions you wish to calculateATOMS18=228,230,237,239the atoms involved for each of the torsions you wish to calculateATOMS19=239,241,244,246the atoms involved for each of the torsions you wish to calculateATOMS20=246,248,254,256the atoms involved for each of the torsions you wish to calculateATOMS21=256,258,273,275the atoms involved for each of the torsions you wish to calculateATOMS22=275,277,280,282the atoms involved for each of the torsions you wish to calculateATOMS23=282,284,291,293the atoms involved for each of the torsions you wish to calculateATOMS24=293,295,303,305the atoms involved for each of the torsions you wish to calculateATOMS25=305,307,322,324the atoms involved for each of the torsions you wish to calculateATOMS26=324,326,329,331the atoms involved for each of the torsions you wish to calculateATOMS27=331,333,341,343the atoms involved for each of the torsions you wish to calculateATOMS28=343,345,351,353the atoms involved for each of the torsions you wish to calculateATOMS29=353,355,368,370the atoms involved for each of the torsions you wish to calculateATOMS30=370,372,379,381the atoms involved for each of the torsions you wish to calculateATOMS31=381,383,394,396the atoms involved for each of the torsions you wish to calculateATOMS32=396,398,409,411the atoms involved for each of the torsions you wish to calculateATOMS33=411,413,421,423the atoms involved for each of the torsions you wish to calculateATOMS34=423,425,438,440the atoms involved for each of the torsions you wish to calculateATOMS35=440,442,457,459the atoms involved for each of the torsions you wish to calculateATOMS36=459,461,474,476the atoms involved for each of the torsions you wish to calculateATOMS37=476,478,484,486the atoms involved for each of the torsions you wish to calculateATOMS38=486,488,494,496the atoms involved for each of the torsions you wish to calculateATOMS39=496,498,510,512the atoms involved for each of the torsions you wish to calculateATOMS40=512,514,524,526the atoms involved for each of the torsions you wish to calculateATOMS41=526,528,541,543the atoms involved for each of the torsions you wish to calculateATOMS42=543,545,552,554the atoms involved for each of the torsions you wish to calculateATOMS43=554,556,571,573the atoms involved for each of the torsions you wish to calculateATOMS44=573,575,586,588the atoms involved for each of the torsions you wish to calculateATOMS45=588,590,600,602the atoms involved for each of the torsions you wish to calculateATOMS46=602,604,616,618the atoms involved for each of the torsions you wish to calculateATOMS47=618,620,640,642the atoms involved for each of the torsions you wish to calculateATOMS48=642,644,654,656the atoms involved for each of the torsions you wish to calculateATOMS49=656,658,666,668the atoms involved for each of the torsions you wish to calculateATOMS50=668,670,685,687the atoms involved for each of the torsions you wish to calculateATOMS51=687,689,707,709the atoms involved for each of the torsions you wish to calculateATOMS52=709,711,721,723the atoms involved for each of the torsions you wish to calculateATOMS53=723,725,736,738the atoms involved for each of the torsions you wish to calculateATOMS54=738,740,743,745the atoms involved for each of the torsions you wish to calculateATOMS55=745,747,765,767the atoms involved for each of the torsions you wish to calculateLABEL=ab ... ALPHABETAa label for the action so that its output can be referenced in the input to other actionsMETAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=metaa label for the action so that its output can be referenced in the input to other actionsARG=rg,abthe input for this action is the scalar output from one or more other actionsSIGMA=0.2,1.0the widths of the Gaussian hillsHEIGHT=0.5the heights of the Gaussian hillsPACE=1000the frequency for hill additionBIASFACTOR=4use well tempered metadynamics and use this bias factorTEMP=298 ... METADthe system temperature - this is only needed if you are doing well-tempered metadynamicsPrint quantities to a file. More detailsARG=rg,ab,meta.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesENDPLUMED# 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 LISTTerminate plumed input. More details#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>