Project ID: plumID:26.007
Source: pcv_metad/plumed_metad_pcv.dat
Originally used with PLUMED version: 2.9
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
#RESTART UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A ENERGYthe units of energy=kcal/mol MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=template.pdb WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=1-5761 ENTITY1the atoms that make up a molecule that you wish to align=5762-5825 p1: PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=REPARAM_fnf.pdb LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=6.06 NEIGH_STRIDEhow often the neighbor list needs to be calculated in time units=4 NEIGH_SIZEsize of the neighbor list=8 ########################################### #### CVs for free-energy reweighting #### ########################################### 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=5816,5817,5819,5821,5823,5824 c2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=5762,5763,5766,5768,5770,5772 CV1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,c2 CV2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c2,525 c3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=5802,5803,5806,5807,5808,5810 ang: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=c1,c3,c2 wall_z: 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=3 KAPPAthe force constant for the wall=1000.0 ############################ #### PCV-Metadynamics #### ############################ METADUsed to performed metadynamics on one or more collective variables. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=meta #RESTART=YES ARGthe labels of the scalars on which the bias will act=p1.sss,p1.zzz SIGMAthe widths of the Gaussian hills=0.15,0.15 HEIGHTthe heights of the Gaussian hills=0.3 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 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] GRID_MINthe lower bounds for the grid=-1,-1 GRID_MAXthe upper bounds for the grid=13,4 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.01,0.01 GRID_WFILEthe file on which to write the grid=grid.dat GRID_WSTRIDEwrite the grid to a file every N steps=50000 FILE a file in which the list of added hills is stored=HILLS ... METAD
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 ENDPLUMEDTerminate plumed input. More details