Project ID: plumID:20.012
Source: fun_SWISH/plumed.dat
Originally used with PLUMED version: 2.4.2
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

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


###############################################
###DEFINE RADIUS + CALC PROT-LIG VECTOR COMP###
###############################################
LOAD FILE=ProjectionOnAxis.cpp
MOLINFO STRUCTURE=5akk_eqPR2_Ct_ALIGN.pdb
INCLUDE FILE=cmap.dat

WHOLEMOLECULES STRIDE=1 ENTITY0=1-5120 ENTITY1=5121-5137

########################
###DEFINITION_OF_COMs###
########################
lig: COM ATOMS=5121-5137		# Ligand - 547 FRG
p2_FS1: COM ATOMS=3019,4303,4718	# 196 SER@CA, 274 VAL@CA, 300 HIS(HIE)@CA
p2_FS2: COM ATOMS=2321,2160,4385,2411	# 152 SER@CA, 141 ILE@CA, 279 MET@CA, 158 VAL@CA
p1: GROUP ATOMS=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_AXIS AXIS_ATOMS=p1,p2_FS2 ATOM=lig



#######################
###FUNNEL_PARAMETERS###
#######################
s_cent: CONSTANT VALUES=3.0      	                              # INFLEXION
beta_cent: CONSTANT VALUES=1.5    	                              # STEEPNESS
wall_width: CONSTANT VALUES=1.2   	                              # WIDTH (h)
wall_buffer: CONSTANT VALUES=0.15  	                              # BUFFER (f, total width = WIDTH + BUFFER)
lwall: LOWER_WALLS ARG=pp.proj AT=0.0 KAPPA=2000.0 EXP=2 EPS=1        # Lower Wall (the starting point of the funnel)
uwall: UPPER_WALLS ARG=pp.proj,cmap AT=4.5,6.0 KAPPA=2000.0,3000.0 EXP=2,2 EPS=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
##################################
MATHEVAL ...
	LABEL=wall_center
	ARG=pp.proj,s_cent,beta_cent,wall_width,wall_buffer
	VAR=s,sc,b,h,f
	FUNC=h*(1./(1.+exp(b*(s-sc))))+f
	PERIODIC=NO
... MATHEVAL


##############################
#####POTENTIAL_PARAMETERS#####
##############################
scaling: CONSTANT VALUES=1.0
spring: CONSTANT VALUES=1000.0

##############################
#######DEFINE_POTENTIAL#######
##############################
MATHEVAL ...
	LABEL=wall_bias
	ARG=pp.ext,spring,wall_center,scaling
	VAR=z,k,zc,sf
	FUNC=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sf)
	PERIODIC=NO
... MATHEVAL

finalbias: BIASVALUE ARG=wall_bias


###############################
########DEFINE_METAD###########
###############################
METAD ...
	LABEL=meta ARG=pp.proj,pp.ext 
	SIGMA=0.025,0.03 HEIGHT=1.5 
	PACE=1000 FILE=HILLS 
        GRID_MIN=-0.5,0.0 GRID_MAX=5.0,2.0 GRID_SPACING=0.005,0.06
	BIASFACTOR=10.0 TEMP=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

PRINT ARG=* STRIDE=1000 FILE=COLVAR FMT=%8.4f