Project ID: plumID:22.000
Source: plumed-1.0.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=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).file to be includedUNITSThis command sets the internal units for the code. More detailsLENGTH=nmthe units of lengthsTIME=psthe units of timeENERGY=kj/molthe units of energyMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=1.pdba file in pdb format containing a reference structureRANDOM_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 detailsATOMS1=5568,5504the atoms involved in each of the contacts you wish to calculateSWITCH1={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT1=0.09091A weight value for a given contact, by default is 1ATOMS2=5546,5491the atoms involved in each of the contacts you wish to calculateSWITCH2={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT2=0.09091A weight value for a given contact, by default is 1ATOMS3=5524,5471the atoms involved in each of the contacts you wish to calculateSWITCH3={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT3=0.09091A weight value for a given contact, by default is 1ATOMS4=5505,5452the atoms involved in each of the contacts you wish to calculateSWITCH4={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT4=0.09091A weight value for a given contact, by default is 1ATOMS5=5492,5438the atoms involved in each of the contacts you wish to calculateSWITCH5={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT5=0.09091A weight value for a given contact, by default is 1ATOMS6=5472,5419the atoms involved in each of the contacts you wish to calculateSWITCH6={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT6=0.09091A weight value for a given contact, by default is 1ATOMS7=5453,5403the atoms involved in each of the contacts you wish to calculateSWITCH7={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT7=0.09091A weight value for a given contact, by default is 1ATOMS8=5439,5384the atoms involved in each of the contacts you wish to calculateSWITCH8={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT8=0.09091A weight value for a given contact, by default is 1ATOMS9=5420,5368the atoms involved in each of the contacts you wish to calculateSWITCH9={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT9=0.09091A weight value for a given contact, by default is 1ATOMS10=5404,5354the atoms involved in each of the contacts you wish to calculateSWITCH10={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT10=0.09091A weight value for a given contact, by default is 1ATOMS11=5385,5344the atoms involved in each of the contacts you wish to calculateSWITCH11={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32}The switching functions to use for each of the contacts in your mapWEIGHT11=0.09091A weight value for a given contact, by default is 1SUMcalculate the sum of all the contacts in the input
The CONTACTMAP action with label hbond calculates the following quantities:antibeta:
Quantity Description hbond.contact By not using SUM or CMDIST each contact will be stored in a component CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=3788,5453the atoms involved in each of the contacts you wish to calculateSWITCH1={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.42}The switching functions to use for each of the contacts in your mapWEIGHT1=0.09091A weight value for a given contact, by default is 1ATOMS2=3788,5471the atoms involved in each of the contacts you wish to calculateSWITCH2={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.45}The switching functions to use for each of the contacts in your mapWEIGHT2=0.09091A weight value for a given contact, by default is 1ATOMS3=3788,5472the atoms involved in each of the contacts you wish to calculateSWITCH3={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.39}The switching functions to use for each of the contacts in your mapWEIGHT3=0.09091A weight value for a given contact, by default is 1ATOMS4=3788,5487the atoms involved in each of the contacts you wish to calculateSWITCH4={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.34}The switching functions to use for each of the contacts in your mapWEIGHT4=0.09091A weight value for a given contact, by default is 1ATOMS5=3769,5487the atoms involved in each of the contacts you wish to calculateSWITCH5={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.45}The switching functions to use for each of the contacts in your mapWEIGHT5=0.09091A weight value for a given contact, by default is 1ATOMS6=3768,5487the atoms involved in each of the contacts you wish to calculateSWITCH6={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.31}The switching functions to use for each of the contacts in your mapWEIGHT6=0.09091A weight value for a given contact, by default is 1ATOMS7=3768,5488the atoms involved in each of the contacts you wish to calculateSWITCH7={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.45}The switching functions to use for each of the contacts in your mapWEIGHT7=0.09091A weight value for a given contact, by default is 1ATOMS8=3768,5505the atoms involved in each of the contacts you wish to calculateSWITCH8={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.31}The switching functions to use for each of the contacts in your mapWEIGHT8=0.09091A weight value for a given contact, by default is 1ATOMS9=3768,5523the atoms involved in each of the contacts you wish to calculateSWITCH9={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.37}The switching functions to use for each of the contacts in your mapWEIGHT9=0.09091A weight value for a given contact, by default is 1ATOMS10=3747,5505the atoms involved in each of the contacts you wish to calculateSWITCH10={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.44}The switching functions to use for each of the contacts in your mapWEIGHT10=0.09091A weight value for a given contact, by default is 1ATOMS11=3747,5523the atoms involved in each of the contacts you wish to calculateSWITCH11={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.29}The switching functions to use for each of the contacts in your mapWEIGHT11=0.09091A weight value for a given contact, by default is 1SUMcalculate the sum of all the contacts in the input
The CONTACTMAP action with label antibeta calculates the following quantities:anti1:
Quantity Description antibeta.contact By not using SUM or CMDIST each contact will be stored in a component ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. More detailsRESIDUES=377,378,379,380,381,382,383,384,32,33,34,35,36,37,38this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedR_0=0.1The r_0 parameter of the switching functionSTRANDS_CUTOFF=1If 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 likeSTYLE=inter The ANTIBETARMSD action with label anti1 calculates the following quantities:Antiparallel beta sheets can either form in a single chain or from a pair of chainsanti2:
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 ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. More detailsRESIDUES=430,431,432,433,434,435,32,33,34,35,36,37this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedR_0=0.1The r_0 parameter of the switching functionSTRANDS_CUTOFF=1If 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 likeSTYLE=interAntiparallel beta sheets can either form in a single chain or from a pair of chains
The ANTIBETARMSD action with label anti2 calculates the following quantities:interact:
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 COORDINATIONCalculate coordination numbers. More detailsGROUPA=3731,3733,3735,3737,3741,3745,3746,3747,3749,3751,3754,3757,3760,3763,3767,3768,3769,3771,3773,3776,3778,3782,3786,3787,3788,3790,3793,3794,4515,4517,4519,4522,4525,4528,4531,4535,4536,4537,4539,4541,4545,4546,4547,4549,4551,4554,4556,4560,4564,4565,4566,4567,4570,4572,4575,4578,4579,4580,4582,4584,4588,4589,4590,4592,4594,4597,4599,4603,4607,4608First list of atomsGROUPB=5472,5474,5476,5478,5482,5486,5487,5488,5490,5492,5495,5498,5499,5503,5504,5505,5507,5509,5512,5514,5518,5522,5523,5524,5526,5528,5531,5534,5540,5544,5545Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.45The r_0 parameter of the switching function
The COORDINATION action with label interact calculates a scalar quantityalpha:ALPHARMSDProbe the alpha helical content of a protein structure. More detailsRESIDUES=28-39this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedR_0=0.1The r_0 parameter of the switching functionD_0=0.02 The ALPHARMSD action with label alpha calculates the following quantities:The d_0 parameter of the switching functionapp_head:
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 CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=5371,5387 app_tail:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=5548,5570 distance:the group of atoms that you are calculating the Gyration Tensor forDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=app_head,app_tail # --- End of included input ---the pair of atom that we are calculating the distance between
The DISTANCE action with label distance calculates a scalar quantitybe0:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=hbondthe input for this action is the scalar output from one or more other actionsSIGMA=0.2the widths of the Gaussian hillsHEIGHT=4.0the heights of the Gaussian hillsBIASFACTOR=20use well tempered metadynamics and use this bias factorTEMP=310the system temperature - this is only needed if you are doing well-tempered metadynamicsPACE=2000the frequency for hill additionFILE=HILLSa file in which the list of added hills is storedGRID_SPACING=0.1the approximate grid spacing (to be used as an alternative or together with GRID_BIN)GRID_MIN=0the lower bounds for the gridGRID_MAX=1.2the upper bounds for the grid
The METAD action with label be0 calculates the following quantities:
Quantity Description be0.bias the instantaneous value of the bias potential Print quantities to a file. More detailsARG=hbond,alpha,distance,antibeta,interact,anti1,anti2the input for this action is the scalar output from one or more other actionsSTRIDE=2000the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=hbond,be0.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=2000the frequency with which the quantities of interest should be outputFILE=BIASthe name of the file on which to output these quantities