Project ID: plumID:19.077
Source: ARG_NH.dat
Originally used with PLUMED version: 2.4
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#RESTART #CVs 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=arg.pdb 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=1-36 #COM from peptide to surface d1 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2332,c1 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 #dist peptide to surface
#restraint wall1 : 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=3.0 KAPPAthe force constant for the wall=1500 #pb 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 SIGMAthe widths of the Gaussian hills=0.05 HEIGHTthe heights of the Gaussian hills=0.2 #kj/mol PACEthe frequency for hill addition=500 BIASFACTORuse well tempered metadynamics and use this bias factor=10 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=0.0 GRID_MAXthe upper bounds for the grid=7.0 LABELa label for the action so that its output can be referenced in the input to other actions=metad FILE a file in which the list of added hills is stored=HILLS.d1 ... METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1.z,metad.bias 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