Project ID: plumID:19.030
Source: plumed_2.dat
Originally used with PLUMED version: 2.5.1
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=1-176
helix1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-88
helix2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=89-176

dist: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix1,helix2

METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=dist SIGMAthe widths of the Gaussian hills=0.05 HEIGHTthe heights of the Gaussian hills=0.05 PACEthe frequency for hill addition=5000 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=323 BIASFACTORuse well tempered metadynamics and use this bias factor=10 GRID_MINthe lower bounds for the grid=-0.5 GRID_MAXthe upper bounds for the grid=7.5 GRID_BINthe number of bins for the grid=400 FILE a file in which the list of added hills is stored=HILLS

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dist ATthe positions of the wall=4.5 KAPPAthe force constant for the wall=3000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dist ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=3000 LABELa label for the action so that its output can be referenced in the input to other actions=lwall

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=100 FILEthe name of the file on which to output these quantities=COLVAR