Project ID: plumID:19.045
Source: Walker_1/plumed.equi.inp
Originally used with PLUMED version: 2.3
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
# Restart command
RESTARTActivate restart. More details

# Units UNITSThis command sets the internal units for the code. More details ENERGYthe units of energy=eV LENGTHthe units of lengths=A TIMEthe units of time=ps # Water oxygens group ow: 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=25205-60049:3 # Position of the adsorbate p1: POSITIONCalculate the components of the position of an atom. More details ATOMthe atom number=1 NOPBC ignore the periodic boundary conditions when calculating distances
# cation-water coordination no c1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=13365 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=ow D_0 The d_0 parameter of the switching function=2.1 R_0The r_0 parameter of the switching function=1.0 NN The n parameter of the switching function =4 MM The m parameter of the switching function; 0 implies 2*NN=10 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=7 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 # Walls free energy - position lwallp1x: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.x ATthe positions of the wall=53.0 KAPPAthe force constant for the wall=1 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 uwallp1x: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.x ATthe positions of the wall=72.0 KAPPAthe force constant for the wall=1 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 lwallp1y: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.y ATthe positions of the wall=32.5 KAPPAthe force constant for the wall=1 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 uwallp1y: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.y ATthe positions of the wall=39.0 KAPPAthe force constant for the wall=1 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 uwallp1z: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.z ATthe positions of the wall=50.0 KAPPAthe force constant for the wall=1 EXP the powers for the walls=4 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 # Metadynamics METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=mtd ARGthe labels of the scalars on which the bias will act=p1.x,p1.z,c1 SIGMAthe widths of the Gaussian hills=0.2,0.2,0.2 PACEthe frequency for hill addition=1000000 HEIGHTthe heights of the Gaussian hills=0.026 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 WALKERS_DIRshared directory with the hills files from all the walkers=../HILLS_DIR WALKERS_RSTRIDEstride for reading hills files=500 WALKERS_Nnumber of walkers=30 WALKERS_IDwalker id=1 ... METAD
# Print CV PRINTPrint quantities to a file. More details ... ARGthe labels of the values that you would like to print to the file=p1.x,p1.y,p1.z,c1,lwallp1x.bias,uwallp1x.bias,lwallp1y.bias,uwallp1y.bias,uwallp1z.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=1000 ... PRINT FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000