Project ID: plumID:22.000
Source: plumed-1.3.dat
Originally used with PLUMED version: 2.5
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
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed-common-1.dat
# INCLUDE FILE=plumed-common-1.dat
The INCLUDE action with label plumed-common-1.dat calculates somethingUNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=nm TIMEthe units of time=ps ENERGYthe units of energy=kj/mol
The UNITS action with label calculates somethingMOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=1.pdb
RANDOM_EXCHANGESSet random pattern for exchanges. More details
hbondThe CONTACTMAP action with label hbond calculates the following quantities:| Quantity | Type | Description |
| hbond | scalar | the sum of all the switching function on all the distances |
: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=5568,5504 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT1A weight value for a given contact, by default is 1=0.09091 ATOMS2the atoms involved in each of the contacts you wish to calculate=5546,5491 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT2A weight value for a given contact, by default is 1=0.09091 ATOMS3the atoms involved in each of the contacts you wish to calculate=5524,5471 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT3A weight value for a given contact, by default is 1=0.09091 ATOMS4the atoms involved in each of the contacts you wish to calculate=5505,5452 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT4A weight value for a given contact, by default is 1=0.09091 ATOMS5the atoms involved in each of the contacts you wish to calculate=5492,5438 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT5A weight value for a given contact, by default is 1=0.09091 ATOMS6the atoms involved in each of the contacts you wish to calculate=5472,5419 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT6A weight value for a given contact, by default is 1=0.09091 ATOMS7the atoms involved in each of the contacts you wish to calculate=5453,5403 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT7A weight value for a given contact, by default is 1=0.09091 ATOMS8the atoms involved in each of the contacts you wish to calculate=5439,5384 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT8A weight value for a given contact, by default is 1=0.09091 ATOMS9the atoms involved in each of the contacts you wish to calculate=5420,5368 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT9A weight value for a given contact, by default is 1=0.09091 ATOMS10the atoms involved in each of the contacts you wish to calculate=5404,5354 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT10A weight value for a given contact, by default is 1=0.09091 ATOMS11the atoms involved in each of the contacts you wish to calculate=5385,5344 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT11A weight value for a given contact, by default is 1=0.09091 SUM calculate the sum of all the contacts in the input
antibetaThe CONTACTMAP action with label antibeta calculates the following quantities:| Quantity | Type | Description |
| antibeta | scalar | the sum of all the switching function on all the distances |
: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=3788,5453 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.42} WEIGHT1A weight value for a given contact, by default is 1=0.09091 ATOMS2the atoms involved in each of the contacts you wish to calculate=3788,5471 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.45} WEIGHT2A weight value for a given contact, by default is 1=0.09091 ATOMS3the atoms involved in each of the contacts you wish to calculate=3788,5472 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.39} WEIGHT3A weight value for a given contact, by default is 1=0.09091 ATOMS4the atoms involved in each of the contacts you wish to calculate=3788,5487 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.34} WEIGHT4A weight value for a given contact, by default is 1=0.09091 ATOMS5the atoms involved in each of the contacts you wish to calculate=3769,5487 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.45} WEIGHT5A weight value for a given contact, by default is 1=0.09091 ATOMS6the atoms involved in each of the contacts you wish to calculate=3768,5487 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.31} WEIGHT6A weight value for a given contact, by default is 1=0.09091 ATOMS7the atoms involved in each of the contacts you wish to calculate=3768,5488 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.45} WEIGHT7A weight value for a given contact, by default is 1=0.09091 ATOMS8the atoms involved in each of the contacts you wish to calculate=3768,5505 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.31} WEIGHT8A weight value for a given contact, by default is 1=0.09091 ATOMS9the atoms involved in each of the contacts you wish to calculate=3768,5523 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.37} WEIGHT9A weight value for a given contact, by default is 1=0.09091 ATOMS10the atoms involved in each of the contacts you wish to calculate=3747,5505 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.44} WEIGHT10A weight value for a given contact, by default is 1=0.09091 ATOMS11the atoms involved in each of the contacts you wish to calculate=3747,5523 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.29} WEIGHT11A weight value for a given contact, by default is 1=0.09091 SUM calculate the sum of all the contacts in the input
anti1The SUM action with label anti1 calculates the following quantities:| Quantity | Type | Description |
| anti1 | scalar | the sum of all the elements in the input vector |
: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=377,378,379,380,381,382,383,384,32,33,34,35,36,37,38 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=inter
anti2The SUM action with label anti2 calculates the following quantities:| Quantity | Type | Description |
| anti2 | scalar | the sum of all the elements in the input vector |
: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=430,431,432,433,434,435,32,33,34,35,36,37 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=inter
interactThe COORDINATION action with label interact calculates the following quantities:| Quantity | Type | Description |
| interact | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3731,3733,3735,3737,3741,3745,3746,3747,3749,3751,3754,3757,3760,3763,3767,3768,3769,3771,3773,3776,3778,3782,3786,3787,3788,3790,3793,3794,4515,4517,4519,4522,4525,4528,4531,4535,4536,4537,4539,4541,4545,4546,4547,4549,4551,4554,4556,4560,4564,4565,4566,4567,4570,4572,4575,4578,4579,4580,4582,4584,4588,4589,4590,4592,4594,4597,4599,4603,4607,4608 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5472,5474,5476,5478,5482,5486,5487,5488,5490,5492,5495,5498,5499,5503,5504,5505,5507,5509,5512,5514,5518,5522,5523,5524,5526,5528,5531,5534,5540,5544,5545 R_0The r_0 parameter of the switching function=0.45
alphaThe SUM action with label alpha calculates the following quantities:| Quantity | Type | Description |
| alpha | scalar | the sum of all the elements in the input vector |
: ALPHARMSDProbe the alpha helical content of a protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=28-39 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 D_0 The d_0 parameter of the switching function=0.02
app_headThe CENTER_FAST action with label app_head calculates the following quantities:| Quantity | Type | Description |
| app_head | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=5371,5387
app_tailThe CENTER_FAST action with label app_tail calculates the following quantities:| Quantity | Type | Description |
| app_tail | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=5548,5570
distanceThe DISTANCE action with label distance calculates the following quantities:| Quantity | Type | Description |
| distance | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=app_head,app_tail
# --- End of included input ---
be3The METAD action with label be3 calculates the following quantities:| Quantity | Type | Description |
| be3.bias | scalar | the instantaneous value of the bias potential |
: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=antibeta SIGMAthe widths of the Gaussian hills=0.2 HEIGHTthe heights of the Gaussian hills=6.0 BIASFACTORuse well tempered metadynamics and use this bias factor=40 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 PACEthe frequency for hill addition=2000 FILE a file in which the list of added hills is stored=HILLS GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1 GRID_MINthe lower bounds for the grid=0 GRID_MAXthe upper bounds for the grid=1.2
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=hbond,alpha,distance,antibeta,interact,anti1,anti2 STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=COLVAR
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=antibeta,be3.bias STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=BIAS
