Project ID: plumID:19.079
Source: nest/ha_doc/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
tested onv2.10
tested onmaster
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=conf.pdb

ene: ENERGYCalculate the total potential energy of the simulation box. More details

#PEPTIDE
pep1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-250
ref: 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=4900
d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ref,pep1 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances

##radius of gyration##
GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=5,28,40,54,66,85,102,114,138,162,177,193,204,219,238 LABELa label for the action so that its output can be referenced in the input to other actions=rg


METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=ene
PACEthe frequency for hill addition=2500 BIASFACTORuse well tempered metadynamics and use this bias factor=10.0 HEIGHTthe heights of the Gaussian hills=2.0
SIGMAthe widths of the Gaussian hills=400
GRID_MINthe lower bounds for the grid=-1700000.0
GRID_MAXthe upper bounds for the grid=-1400000.0
FILE a file in which the list of added hills is stored=HILLS
... METAD


#MTD
METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=d1.z,rg
PACEthe frequency for hill addition=500 BIASFACTORuse well tempered metadynamics and use this bias factor=10.0 HEIGHTthe heights of the Gaussian hills=2.0
SIGMAthe widths of the Gaussian hills=0.01,0.02
GRID_MINthe lower bounds for the grid=0.0,0.0
GRID_MAXthe upper bounds for the grid=10.0,10.0
FILE a file in which the list of added hills is stored=HILLS_MTD
LABELa label for the action so that its output can be referenced in the input to other actions=cvbias
... METAD


## wall 
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.z ATthe positions of the wall=4.5 KAPPAthe force constant for the wall=50000 LABELa label for the action so that its output can be referenced in the input to other actions=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=500 FILEthe name of the file on which to output these quantities=COLVAR