PLUMED-NEST

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

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

The WHOLEMOLECULES action with label  calculates somethingallThe GROUP action with label all calculates the following quantities:
 Quantity   
 Type   
 Description  
all
atoms
indices of atoms specified in GROUP:  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

rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the radius of gyration:   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=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential
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=lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential

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=abThe ALPHABETA action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=1,5,8,10    REFERENCE=-0.78540
# ATOMS2=10,12,20,22
# ATOMS3=22,24,39,41
# ATOMS4=41,43,50,52
# ATOMS5=52,54,57,59
# ATOMS6=59,61,74,76
# ATOMS7=76,78,85,87
# ATOMS8=87,89,96,98
# ATOMS9=98,100,113,115
# ATOMS10=115,119,127,129
# ATOMS11=129,131,138,140
# ATOMS12=140,142,153,155
# ATOMS13=155,157,177,179
# ATOMS14=179,183,191,193
# ATOMS15=193,195,201,203
# ATOMS16=203,205,215,217
# ATOMS17=217,219,226,228
# ATOMS18=228,230,237,239
# ATOMS19=239,241,244,246
# ATOMS20=246,248,254,256
# ATOMS21=256,258,273,275
# ATOMS22=275,277,280,282
# ATOMS23=282,284,291,293
# ATOMS24=293,295,303,305
# ATOMS25=305,307,322,324
# ATOMS26=324,326,329,331
# ATOMS27=331,333,341,343
# ATOMS28=343,345,351,353
# ATOMS29=353,355,368,370
# ATOMS30=370,372,379,381
# ATOMS31=381,383,394,396
# ATOMS32=396,398,409,411
# ATOMS33=411,413,421,423
# ATOMS34=423,425,438,440
# ATOMS35=440,442,457,459
# ATOMS36=459,461,474,476
# ATOMS37=476,478,484,486
# ATOMS38=486,488,494,496
# ATOMS39=496,498,510,512
# ATOMS40=512,514,524,526
# ATOMS41=526,528,541,543
# ATOMS42=543,545,552,554
# ATOMS43=554,556,571,573
# ATOMS44=573,575,586,588
# ATOMS45=588,590,600,602
# ATOMS46=602,604,616,618
# ATOMS47=618,620,640,642
# ATOMS48=642,644,654,656
# ATOMS49=656,658,666,668
# ATOMS50=668,670,685,687
# ATOMS51=687,689,707,709
# ATOMS52=709,711,721,723
# ATOMS53=723,725,736,738
# ATOMS54=738,740,743,745
# ATOMS55=745,747,765,767
#  LABEL=ab
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
ab_torsionsThe TORSION action with label ab_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=1,5,8,10 ATOMS2the four atoms involved in the torsional angle=10,12,20,22 ATOMS3the four atoms involved in the torsional angle=22,24,39,41 ATOMS4the four atoms involved in the torsional angle=41,43,50,52 ATOMS5the four atoms involved in the torsional angle=52,54,57,59     # Action input conctinues with 50 further ATOMSn keywords, 
ab_refThe CONSTANT action with label ab_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540,-0.78540
ab_coeffThe CONSTANT action with label ab_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
ab_combThe COMBINE action with label ab_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ab_torsions,ab_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab_cosThe CUSTOM action with label ab_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ab_comb,ab_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
abThe SUM action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=ab_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
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=metaThe METAD action with label meta calculates the following quantities:
 Quantity   
 Type   
 Description  
meta.bias
scalar
the instantaneous value of the bias potential
  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
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. 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
 FILE a file in which the list of added hills is stored=HILLS
... 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