Project ID: plumID:19.077
Source: 12mer_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 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=12mer.pdb #PEPTIDE DISTANCE# 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=1-197 d1 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2473,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=5,29,51,72,84,96,108,120,127,144,161,175 LABELa label for the action so that its output can be referenced in the input to other actions=rg
##ENERGY## ene : ENERGYCalculate the total potential energy of the simulation box. More details
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=6.0 KAPPAthe force constant for the wall=1500 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=5000 BIASFACTORuse well tempered metadynamics and use this bias factor=25.0 HEIGHTthe heights of the Gaussian hills=2.0 SIGMAthe widths of the Gaussian hills=300 GRID_MINthe lower bounds for the grid=-5350000.000000 GRID_MAXthe upper bounds for the grid=-5250000.000000 FILE a file in which the list of added hills is stored=HILLS ... METAD
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=250 BIASFACTORuse well tempered metadynamics and use this bias factor=25.0 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=20.0,10.0 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ene 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