PLUMED-NEST

Project ID: plumID:20.025
Source: OAH_alone/plumed.dat
Originally used with PLUMED version: 2.5
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

# --- (1) ATOMS DEFINITIONS and ALIGNMENT ---

HOSTThe GROUP action with label HOST calculates the following quantities:
 Quantity   
 Type   
 Description  
HOST
atoms
indices of atoms specified in GROUP: 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=1-184      #host atoms
WOThe GROUP action with label WO calculates the following quantities:
 Quantity   
 Type   
 Description  
WO
atoms
indices of atoms specified in GROUP: 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=193-6492:3    #water oxygen atoms

WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=HOST
The WHOLEMOLECULES action with label  calculates somethingFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details STRIDE the frequency with which molecules are reassembled=1 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=conf_template.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL #coordinates alignment

v1The FIXEDATOM action with label v1 calculates the following quantities:
 Quantity   
 Type   
 Description  
v1
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.0   #virtual atoms
v1: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.0   #virtual atoms  SET_MASS=1 SET_CHARGE=0
v2The FIXEDATOM action with label v2 calculates the following quantities:
 Quantity   
 Type   
 Description  
v2
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.25
v2: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.25  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
v3The FIXEDATOM action with label v3 calculates the following quantities:
 Quantity   
 Type   
 Description  
v3
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.5
v3: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.5  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
v4The FIXEDATOM action with label v4 calculates the following quantities:
 Quantity   
 Type   
 Description  
v4
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.75
v4: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.75  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
v5The FIXEDATOM action with label v5 calculates the following quantities:
 Quantity   
 Type   
 Description  
v5
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.0
v5: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.0  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
v6The FIXEDATOM action with label v6 calculates the following quantities:
 Quantity   
 Type   
 Description  
v6
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.25
v6: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.25  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
v7The FIXEDATOM action with label v7 calculates the following quantities:
 Quantity   
 Type   
 Description  
v7
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.5
v7: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.5  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
v8The FIXEDATOM action with label v8 calculates the following quantities:
 Quantity   
 Type   
 Description  
v8
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.75
v8: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.75  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0

# --- (2) DESCRIPTORS ---

#V1: COORDINATION GROUPA=v1 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
V2The COORDINATION action with label V2 calculates the following quantities:
 Quantity   
 Type   
 Description  
V2
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
#V3: COORDINATION GROUPA=v3 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
#V4: COORDINATION GROUPA=v4 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
#V5: COORDINATION GROUPA=v5 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
#V6: COORDINATION GROUPA=v6 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
#V7: COORDINATION GROUPA=v7 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
#V8: COORDINATION GROUPA=v8 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5

# --- (3) DEEP-LDA CV and other quantities ---

eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details

# --- (4) OPES  ---

OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. 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=opesThe OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential
opes.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff
scalar
effective sample size
opes.nker
scalar
total number of compressed kernels used to represent the bias
   ARGthe labels of the scalars on which the bias will act=V2
   FILE a file in which the list of all deposited kernels is stored=Kernels.data
   PACEthe frequency for kernel deposition=500
   BARRIERthe free energy barrier to be overcome=50
   RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
   STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed_Kernels.data
   STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed_Kernels.data
   STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=50000
   #WALKERS_MPI
... OPES_METAD
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
   LABELa label for the action so that its output can be referenced in the input to other actions=opes
   ARGthe labels of the scalars on which the bias will act=V2
   FILE a file in which the list of all deposited kernels is stored=Kernels.data
   PACEthe frequency for kernel deposition=500
   BARRIERthe free energy barrier to be overcome=50
   RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
   STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed_Kernels.data
   STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed_Kernels.data
   STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=50000
   #WALKERS_MPI
 TEMP temperature=-1 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_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=250 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f

ENDPLUMEDTerminate plumed input. More details