Project ID: plumID:26.010
Source: NH3_form/plumed.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
tested onv2.10
tested onmaster
# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
#RESTART
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=0.001  #Amstroeng, kJ/mol, fs

INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=./group_indices.dat

dnh: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=N GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H MAXcalculate the maximum value={BETA=0.05} MINcalculate the minimum value={BETA=20.0}

c1: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=N SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=H R_0The r_0 parameter of the switching function=2.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.05} MINcalculate the minimum value={BETA=20.0}
c2: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=N SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=Li R_0The r_0 parameter of the switching function=4.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.05} MINcalculate the minimum value={BETA=20.0}

c3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=Na R_0The r_0 parameter of the switching function=3.5
c4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=Li R_0The r_0 parameter of the switching function=3.5
cnali: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c3,c4 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

cnh1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=4002 R_0The r_0 parameter of the switching function=2.0
cnh2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=4003 R_0The r_0 parameter of the switching function=2.0 
cnh3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=4004 R_0The r_0 parameter of the switching function=2.0 

ctot: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cnh1,cnh2,cnh3 FUNCthe function you wish to evaluate=x+y+z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dnh.max ATthe positions of the wall=6.0 KAPPAthe force constant for the wall=200.0 EXP the powers for the walls=2.0


OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
   LABELa label for the action so that its output can be referenced in the input to other actions=opes1
   ARGthe labels of the scalars on which the bias will act=ctot
   FILE a file in which the list of all deposited kernels is stored=Kernels1.data
   TEMP temperature=600
   PACEthe frequency for kernel deposition=200
   BARRIERthe free energy barrier to be overcome=250
   RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
   #EXCLUDED_REGION=t1
... OPES_METAD_EXPLORE

OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
   LABELa label for the action so that its output can be referenced in the input to other actions=opes2
   ARGthe labels of the scalars on which the bias will act=c4
   FILE a file in which the list of all deposited kernels is stored=Kernels2.data
   TEMP temperature=600
   PACEthe frequency for kernel deposition=500
   BARRIERthe free energy barrier to be overcome=80
   RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
   #EXCLUDED_REGION=t1
... OPES_METAD_EXPLORE


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=50 FILEthe name of the file on which to output these quantities=COLVAR
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=1