Project ID: plumID:21.026
Source: plumed_input/plumed.dat
Originally used with PLUMED version: 2.4
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
UNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengthsENERGY=kcal/molthe units of energyWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-5946the atoms that make up a molecule that you wish to align
dist:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1614,5843 dist2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2838,3207 dist3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=473,5093 dist4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=473,5843 #between Lys(N+)374 and com of ASP21 ASP65the pair of atom that we are calculating the distance betweenCOMCalculate the center of mass for a group of atoms. More detailsATOMS=351,1038the list of atoms which are involved the virtual atom's definitionLABEL=coo dist5:a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5767,coothe pair of atom that we are calculating the distance between
path1:PATHMSDThis Colvar calculates path collective variables. More detailsREFERENCE=reference_path-renumb.pdbthe pdb is needed to provide the various milestonesLAMBDA=1.46the lambda parameter is needed for smoothing, is in the units of plumedNEIGH_STRIDE=100how often the neighbor list needs to be calculated in time unitsNEIGH_SIZE=20size of the neighbor listMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=path1.sss,path1.zzzthe input for this action is the scalar output from one or more other actionsPACE=400the frequency for hill additionHEIGHT=0.1the heights of the Gaussian hillsSIGMA=1,0.15the widths of the Gaussian hillsFILE=HILLSa file in which the list of added hills is storedBIASFACTOR=50.0use well tempered metadynamics and use this bias factorTEMP=300.0the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=-10,-5the lower bounds for the gridGRID_MAX=100,15 ... METADthe upper bounds for the gridUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=path1.zzzthe arguments on which the bias is actingAT=9.0the positions of the wallKAPPA=100the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallLABEL=uwalla label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsSTRIDE=200the frequency with which the quantities of interest should be outputARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantities