PLUMED-NEST

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
# The command:
# INCLUDE FILE=plumed-common-1.dat
# ensures PLUMED loads the contents of the file called plumed-common-1.dat
# The contents of this file are shown below (click the red comment to hide them).
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

hbond: 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 

The CONTACTMAP action with label hbond calculates the following quantities:
 Quantity   
 Description  
hbond.contact
By not using SUM or CMDIST each contact will be stored in a component
hbond.value
the sum of all the switching function on all the distancesantibeta: 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

The CONTACTMAP action with label antibeta calculates the following quantities:
 Quantity   
 Description  
antibeta.contact
By not using SUM or CMDIST each contact will be stored in a component
antibeta.value
the sum of all the switching function on all the distancesanti1: 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
The ANTIBETARMSD action with label anti1 calculates the following quantities:
 Quantity   
 Description  
anti1.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
anti1.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
anti1.value
if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheetanti2: 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

The ANTIBETARMSD action with label anti2 calculates the following quantities:
 Quantity   
 Description  
anti2.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
anti2.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
anti2.value
if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheetinteract: 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

The COORDINATION action with label interact calculates the following quantities:
 Quantity   
 Description  
interact.value
the value of the coordinationalpha: 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
The ALPHARMSD action with label alpha calculates the following quantities:
 Quantity   
 Description  
alpha.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
alpha.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helixapp_head: 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
The CENTER action with label app_head calculates the following quantities:
 Quantity   
 Description  
app_head.value
the position of the center of massapp_tail: 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
The CENTER action with label app_tail calculates the following quantities:
 Quantity   
 Description  
app_tail.value
the position of the center of massdistance: 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 --- 
The DISTANCE action with label distance calculates the following quantities:
 Quantity   
 Description  
distance.value
the DISTANCE between this pair of atomsbe3: 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

The METAD action with label be3 calculates the following quantities:
 Quantity   
 Description  
be3.bias
the instantaneous value of the bias potentialPRINTPrint 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