PLUMED-NEST-TEST-SITE

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

Click on the labels of the actions for more information on what each action computes

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#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 it

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###
########################
The WHOLEMOLECULES action with label  calculates somethingligThe COM action with label lig calculates the following quantities:
 Quantity   
 Type   
 Description  
lig
atoms
virtual atom calculated by COM action: 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_FS1The COM action with label p2_FS1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p2_FS1
atoms
virtual atom calculated by COM action: 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_FS2The COM action with label p2_FS2 calculates the following quantities:
 Quantity   
 Type   
 Description  
p2_FS2
atoms
virtual atom calculated by COM action: 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
p1The GROUP action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1
atoms
indices of atoms specified in GROUP: 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###
##############################
ppThe PROJECTION_ON_AXIS action with label pp calculates the following quantities:
 Quantity   
 Type   
 Description  
pp.proj
scalar
The value of the projection along the axis
pp.ext
scalar
The value of the extension from the axis: 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_centThe CONSTANT action with label s_cent calculates the following quantities:
 Quantity   
 Type   
 Description  
s_cent
scalar
the constant value that was read from the plumed input: 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
s_cent: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=3.0      	                              # INFLEXION  NROWS=0 NCOLS=0
beta_centThe CONSTANT action with label beta_cent calculates the following quantities:
 Quantity   
 Type   
 Description  
beta_cent
scalar
the constant value that was read from the plumed input: 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
beta_cent: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1.5    	                              # STEEPNESS  NROWS=0 NCOLS=0
wall_widthThe CONSTANT action with label wall_width calculates the following quantities:
 Quantity   
 Type   
 Description  
wall_width
scalar
the constant value that was read from the plumed input: 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_width: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1.2   	                              # WIDTH (h)  NROWS=0 NCOLS=0
wall_bufferThe CONSTANT action with label wall_buffer calculates the following quantities:
 Quantity   
 Type   
 Description  
wall_buffer
scalar
the constant value that was read from the plumed input: 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)
wall_buffer: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.15  	                              # BUFFER (f, total width = WIDTH + BUFFER)  NROWS=0 NCOLS=0
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 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)
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 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 ATthe positions of the wall=4.5 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 	      # Upper Wall (the ending point of the funnel)


##################################
###########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_centerThe MATHEVAL action with label wall_center calculates the following quantities:
 Quantity   
 Type   
 Description  
wall_center
scalar
an arbitrary function
	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#####
##############################
scalingThe CONSTANT action with label scaling calculates the following quantities:
 Quantity   
 Type   
 Description  
scaling
scalar
the constant value that was read from the plumed input: 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
scaling: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1.0  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
springThe CONSTANT action with label spring calculates the following quantities:
 Quantity   
 Type   
 Description  
spring
scalar
the constant value that was read from the plumed input: 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
spring: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1000.0  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=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_biasThe MATHEVAL action with label wall_bias calculates the following quantities:
 Quantity   
 Type   
 Description  
wall_bias
scalar
an arbitrary function
	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

finalbiasThe BIASVALUE action with label finalbias calculates the following quantities:
 Quantity   
 Type   
 Description  
finalbias.bias
scalar
the instantaneous value of the bias potential
finalbias.wall_bias_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named wall_bias: 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=metaThe METAD action with label meta calculates the following quantities:
 Quantity   
 Type   
 Description  
meta.bias
scalar
the instantaneous value of the bias potential 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_MIN=-0.5,0.0 GRID_MAX=5.0,2.0 GRID_SPACING=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