Project ID: plumID:22.019
Source: fun_path_plm/plumed.dat
Originally used with PLUMED version: 2.7
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
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ...
	ENTITY0the atoms that make up a molecule that you wish to align=1-5148 #protein
	ENTITY1the atoms that make up a molecule that you wish to align=5149-5206 #ligand EB13
... WHOLEMOLECULES

c1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3313,516 # aspartic diad ASP214CG, ASH34CG
c2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=5159,5160 # ligand transition state mimetic nitrogens NAQ, NAR (NAQ=N11, NAR=N12)
d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,c2 # distance between catalytic site and transition state mimetic

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=5149-5206

PATHMSDThis Colvar calculates path collective variables. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=p1
	REFERENCEthe pdb is needed to provide the various milestones=path_ref.pdb
	LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=777.9
	NEIGH_STRIDEhow often the neighbor list needs to be calculated in time units=4
	NEIGH_SIZEsize of the neighbor list=5
... PATHMSD

FUNNEL_PSFUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=fps
	LIGANDThis MUST be a single atom, normally the COM of the ligand=lig
	REFERENCEa file in pdb format containing the structure you would like to align=fun_ref.pdb
	ANCHORClosest protein atom to the ligand, picked to avoid pbc problems during the simulation=511 #ASH34CA
	POINTS6 values defining x, y, and z of the 2 points used to construct the line=7.361,6.649,3.083,7.392,5.482,4.555
... FUNNEL_PS

FUNNELCalculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. This action has hidden defaults. More details ...
	ARGthe labels of the scalars on which the bias will act=fps.lp,fps.ld
	ZCC switching point between cylinder and cone=2.0
	ALPHAangle to change the width of the cone section=0.5
	RCYLradius of the cylindrical section=0.1
	MINSminimum value assumed by fps=-0.5
	MAXS maximum value assumed by fps=4.5
	KAPPAconstant to be used for the funnel-shape restraint potential=35100
	NBINSnumber of bins along fps=500
	NBINZnumber of bins along fps=500
	FILEname of the Funnel potential file=BIAS
	LABELa label for the action so that its output can be referenced in the input to other actions=funnel
... FUNNEL

METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
	ARGthe labels of the scalars on which the bias will act=d1,p1.sss,p1.zzz
	SIGMAthe widths of the Gaussian hills=0.03,0.5,0.01
	HEIGHTthe heights of the Gaussian hills=5.0
	PACEthe frequency for hill addition=500
	TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298
	BIASFACTORuse well tempered metadynamics and use this bias factor=15
	GRID_MINthe lower bounds for the grid=-1.0,0,0
	GRID_MAXthe upper bounds for the grid=5.0,9.0,0.5
	GRID_BINthe number of bins for the grid=1200,200,200
	CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
	LABELa label for the action so that its output can be referenced in the input to other actions=metad
... METAD

LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=fps.lp ATthe positions of the wall=-0.2 KAPPAthe force constant for the wall=50000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=fps.lp-lwall
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=fps.lp ATthe positions of the wall=4.0 KAPPAthe force constant for the wall=50000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=fps.lp-uwall
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=4.0 KAPPAthe force constant for the wall=50000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=d1-uwall
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.zzz ATthe positions of the wall=0.05 KAPPAthe force constant for the wall=500000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=path_rmsd-uwall

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=10
	FILEthe name of the file on which to output these quantities=COLVAR
	FMTthe format that should be used to output real numbers=%8.4f
... PRINT