PLUMED-NEST-TEST-SITE

Project ID: plumID:23.019
Source: plm_path_sketchmap/path/plumed.dat
Originally used with PLUMED version: 2.7.2
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

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=1-6304 # plm5
	ENTITY1the atoms that make up a molecule that you wish to align=6305-6353 # lig
... WHOLEMOLECULES

The WHOLEMOLECULES action with label  calculates somethingPATHMSDThis 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=p1The PATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1.sss
scalar
the position on the path
p1.zzz
scalar
the distance from the path
	REFERENCEthe pdb is needed to provide the various milestones=path_15f.pdb
	LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=961 # lambda=2.3/(average_RMSD_between_frames)**2    2.3/0.048907^2
	NEIGH_SIZEsize of the neighbor list=5
... PATHMSD

METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
	ARGthe labels of the scalars on which the bias will act=p1.sss,p1.zzz
	SIGMAthe widths of the Gaussian hills=0.1,0.001
	HEIGHTthe heights of the Gaussian hills=3.0
	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=10
	GRID_MINthe lower bounds for the grid=-1,-0.1
	GRID_MAXthe upper bounds for the grid=16,0.2
	GRID_BINthe number of bins for the grid=400,800
	CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
	FMTspecify format for HILLS files (useful for decrease the number of digits in regtests)=%8.4f
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=metad
	ARGthe labels of the scalars on which the bias will act=p1.sss,p1.zzz
	SIGMAthe widths of the Gaussian hills=0.1,0.001
	HEIGHTthe heights of the Gaussian hills=3.0
	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=10
	GRID_MINthe lower bounds for the grid=-1,-0.1
	GRID_MAXthe upper bounds for the grid=16,0.2
	GRID_BINthe number of bins for the grid=400,800
	CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
	FMTspecify format for HILLS files (useful for decrease the number of digits in regtests)=%8.4f
 FILE a file in which the list of added hills is stored=HILLS
... METAD

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=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=p1-zzz_uwallThe UPPER_WALLS action with label p1-zzz_uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
p1-zzz_uwall.bias
scalar
the instantaneous value of the bias potential
p1-zzz_uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential

PRINTPrint quantities to a file. More details ...
	STRIDE the frequency with which the quantities of interest should be output=25
	ARGthe labels of the values that you would like to print to the file=*
	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