**Project ID:** plumID:20.012

**Source:** fun_metaD/plumed.dat

**Originally used with PLUMED version:** 2.4.2

**Stable:** zipped raw stdout - zipped raw stderr - stderr

**Master:** zipped raw stdout - zipped raw stderr - stderr

##################################### #plumed.dat for Funnel MetaD + SWISH# ##################################### #RESTART

############################################### ###DEFINE RADIUS + CALC PROT-LIG VECTOR COMP### ############################################### #LOAD FILE=ProjectionOnAxis.cpp # Now part of Plumed, not necessary to load itWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsSTRIDE=1the frequency with which molecules are reassembledENTITY0=1-5120the atoms that make up a molecule that you wish to alignENTITY1=5121-5137the atoms that make up a molecule that you wish to align

######################## ###DEFINITION_OF_COMs### ########################lig:COMCalculate the center of mass for a group of atoms. More detailsATOMS=5121-5137 # Ligand - 547 FRGthe list of atoms which are involved the virtual atom's definitionp2_FS1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=3019,4303,4718 # 196 SER@CA, 274 VAL@CA, 300 HIS(HIE)@CAthe list of atoms which are involved the virtual atom's definitionp2_FS2:COMCalculate the center of mass for a group of atoms. More detailsATOMS=2321,2160,4385,2411 # 152 SER@CA, 141 ILE@CA, 279 MET@CA, 158 VAL@CAthe list of atoms which are involved the virtual atom's definitionp1:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=3728 # 241 TRP@CAthe numerical indexes for the set of atoms in the group

######################## ###DEFINITION_OF_ARGs### ######################## # CV1: pp.proj = projection on the axis. The distance from the axis to the origin (along the axis) # CV2: pp.ext = orthogonal distance between the ATOM(=lig) to the axis. # CV3: ener = energy for the well-tempered ensemble. NOT for plain metaD. ############################## ###PoA_CV_for_Funnel_Side-1### ############################## #pp: PROJECTION_ON_AXIS AXIS_ATOMS=p1,p2_FS1 ATOM=lig

############################## ###PoA_CV_for_Funnel_Side-2### ##############################pp:PROJECTION_ON_AXISCalculate a position based on the projection along and extension from a defined axis. More detailsAXIS_ATOMS=The atoms that define the direction of the axis of interestp1,p2_FS2ATOM=The atom whose position we want to project on the axis of interestlig

####################### ###FUNNEL_PARAMETERS### #######################s_cent:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=3.0 # INFLEXIONThe values of the constantsbeta_cent:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=1.5 # STEEPNESSThe values of the constantswall_width:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=1.2 # WIDTH (h)The values of the constantswall_buffer:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=0.15 # BUFFER (f, total width = WIDTH + BUFFER)The values of the constantslwall:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionspp.projAT=0.0the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2the powers for the wallsEPS=1 # Lower Wall (the starting point of the funnel)the values for s_i in the expression for a walluwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionspp.projAT=4.5the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2the powers for the wallsEPS=1 # Upper Wall (the ending point of the funnel)the values for s_i in the expression for a wall

################################## ###########CALCULATE FUNNEL####### # Returns the radius of the funnel # at the current value of the cv ##################################MATHEVAL...An alias to the ef CUSTOM function. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionswall_centerARG=the input for this action is the scalar output from one or more other actionspp.proj,s_cent,beta_cent,wall_width,wall_bufferVAR=s,sc,b,h,fthe names to give each of the arguments in the functionFUNC=h*(1./(1.+exp(b*(s-sc))))+fthe function you wish to evaluatePERIODIC=NO ... MATHEVALif the output of your function is periodic then you should specify the periodicity of the function

############################## #####POTENTIAL_PARAMETERS##### ##############################scaling:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=1.0The values of the constantsspring:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=1000.0The values of the constants

############################## #######DEFINE_POTENTIAL####### ##############################MATHEVAL...An alias to the ef CUSTOM function. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionswall_biasARG=the input for this action is the scalar output from one or more other actionspp.ext,spring,wall_center,scalingVAR=z,k,zc,sfthe names to give each of the arguments in the functionFUNC=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sfthe function you wish to evaluatePERIODIC=NO ... MATHEVALif the output of your function is periodic then you should specify the periodicity of the functionfinalbias:BIASVALUETakes the value of one variable and use it as a bias More detailsARG=the input for this action is the scalar output from one or more other actionswall_bias

############################### ########DEFINE_METAD########### ###############################METAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsmetaARG=the input for this action is the scalar output from one or more other actionspp.proj,pp.extSIGMA=0.025,0.03the widths of the Gaussian hillsHEIGHT=1.5the heights of the Gaussian hillsPACE=1000the frequency for hill additionFILE=HILLS #GRID_MIN=-0.5,0.0 GRID_MAX=5.0,2.0 GRID_SPACING=0.005,0.06a file in which the list of added hills is storedBIASFACTOR=10.0use well tempered metadynamics and use this bias factorTEMP=300 #REWEIGHTING_NGRID=1120,40 #REWEIGHTING_NHILLS=20 ... METAD #GRID_MIN=0.0,0.0 GRID_MAX=2.0,2.0 GRID_BIN=160,133the system temperature - this is only needed if you are doing well-tempered metadynamicsPrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesFMT=%8.4fthe format that should be used to output real numbers