Project ID: plumID:20.012
Source: fun_SWISH/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

Click on the labels of the actions for more information on what each action computes
tested onv2.10
tested onmaster
tested on master
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#plumed.dat for Funnel MetaD + SWISH#
#####################################
#RESTART


###############################################
###DEFINE RADIUS + CALC PROT-LIG VECTOR COMP###
###############################################
#LOAD FILE=ProjectionOnAxis.cpp
MOLINFOThis 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=5akk_eqPR2_Ct_ALIGN.pdb
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cmap.dat  # This cmap was generated later, it doesn't correspond entirely to the original one

WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=1-5120 ENTITY1the atoms that make up a molecule that you wish to align=5121-5137

########################
###DEFINITION_OF_COMs###
########################
lig: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=5121-5137		# Ligand - 547 FRG
p2_FS1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3019,4303,4718	# 196 SER@CA, 274 VAL@CA, 300 HIS(HIE)@CA
p2_FS2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2321,2160,4385,2411	# 152 SER@CA, 141 ILE@CA, 279 MET@CA, 158 VAL@CA
p1: 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 details ATOMSthe numerical indexes for the set of atoms in the group=3728			# 241 TRP@CA

########################
###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 details AXIS_ATOMSThe atoms that define the direction of the axis of interest=p1,p2_FS2 ATOMThe atom whose position we want to project on the axis of interest=lig



#######################
###FUNNEL_PARAMETERS###
#######################
s_cent: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=3.0      	                              # INFLEXION
beta_cent: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1.5    	                              # STEEPNESS
wall_width: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1.2   	                              # WIDTH (h)
wall_buffer: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.15  	                              # BUFFER (f, total width = WIDTH + BUFFER)
lwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.proj ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1        # Lower Wall (the starting point of the funnel)
uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.proj,cmap ATthe positions of the wall=4.5,6.0 KAPPAthe force constant for the wall=2000.0,3000.0 EXP the powers for the walls=2,2 EPS the values for s_i in the expression for a wall=1,1 # Upper Wall (the ending point of the funnel+restraint_4_swish)


##################################
###########CALCULATE FUNNEL#######
# Returns the radius of the funnel
# at the current value of the cv
##################################
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=wall_center
	ARGthe values input to this function=pp.proj,s_cent,beta_cent,wall_width,wall_buffer
	VARthe names to give each of the arguments in the function=s,sc,b,h,f
	FUNCthe function you wish to evaluate=h*(1./(1.+exp(b*(s-sc))))+f
	PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL


##############################
#####POTENTIAL_PARAMETERS#####
##############################
scaling: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1.0
spring: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1000.0

##############################
#######DEFINE_POTENTIAL#######
##############################
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=wall_bias
	ARGthe values input to this function=pp.ext,spring,wall_center,scaling
	VARthe names to give each of the arguments in the function=z,k,zc,sf
	FUNCthe function you wish to evaluate=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sf)
	PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

finalbias: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=wall_bias


###############################
########DEFINE_METAD###########
###############################
METADUsed to performed metadynamics on one or more collective variables. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=meta ARGthe labels of the scalars on which the bias will act=pp.proj,pp.ext 
	SIGMAthe widths of the Gaussian hills=0.025,0.03 HEIGHTthe heights of the Gaussian hills=1.5 
	PACEthe frequency for hill addition=1000 FILE a file in which the list of added hills is stored=HILLS 
        GRID_MINthe lower bounds for the grid=-0.5,0.0 GRID_MAXthe upper bounds for the grid=5.0,2.0 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.005,0.06
	BIASFACTORuse well tempered metadynamics and use this bias factor=10.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300	
	
	#REWEIGHTING_NGRID=1120,40
	#REWEIGHTING_NHILLS=20
... METAD
#GRID_MIN=0.0,0.0 GRID_MAX=2.0,2.0 GRID_BIN=160,133

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f