Project ID: plumID:19.020
Source: step-1/plumed.0.dat
Originally used with PLUMED version: 2.2
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=reference.pdba file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsSTRIDE=1the frequency with which molecules are reassembledENTITY0=1-427the atoms that make up a molecule that you wish to align
a:ALPHARMSDProbe the alpha helical content of a protein structure. More detailsRESIDUES=allthis command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=DRMSDthe manner in which RMSD alignment is performedR_0=0.08The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12 g:The m parameter of the switching functionGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=9,23,35,50,62,78,89,101,120,135,159,183,202,212,229,253,272,282,297,321,345,362,377,389,400,410 ene:the group of atoms that you are calculating the Gyration Tensor forENERGYCalculate the total potential energy of the simulation box. More details
wte:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=enethe input for this action is the scalar output from one or more other actionsPACE=250the frequency for hill additionHEIGHT=2.5the heights of the Gaussian hillsSIGMA=500.0the widths of the Gaussian hillsFILE=HILLS_PTWTEa file in which the list of added hills is storedBIASFACTOR=50.0use well tempered metadynamics and use this bias factorTEMP=298.0the system temperature - this is only needed if you are doing well-tempered metadynamicsPrint quantities to a file. More detailsARG=a,g,ene,wte.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=50the frequency with which the quantities of interest should be outputFILE=COLVAR_WTEthe name of the file on which to output these quantitiesENDPLUMEDTerminate plumed input. More details